diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 2468 |
1 files changed, 1427 insertions, 1041 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0856162440..cb441655eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -59,7 +59,7 @@ #:use-module (gnu packages statistics) #:use-module (gnu packages web) #:use-module (gnu packages xml) - #:use-module (srfi srfi-1)) + #:use-module ((srfi srfi-1) #:hide (zip))) ;;; Annotations @@ -1734,13 +1734,13 @@ methylation arrays.") (define-public r-missmethyl (package (name "r-missmethyl") - (version "1.32.1") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "missMethyl" version)) (sha256 (base32 - "1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma")))) + "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h")))) (properties `((upstream-name . "missMethyl"))) (build-system r-build-system) (propagated-inputs @@ -2032,13 +2032,13 @@ and @code{Sailfish}. Alevin example output is also included.") (define-public r-abarray (package (name "r-abarray") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABarray" version)) (sha256 (base32 - "02rjxzbrzphl28z8zpgw3gavzlzlx71n5ld8sb3im6xpn81ykvfh")))) + "0vrsyx06acdkb3hq350zdnx3bqzz43grf1w8n0pmxlcr2dncchv9")))) (properties `((upstream-name . "ABarray"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest)) @@ -2058,13 +2058,13 @@ into folders according to the analysis settings used.") (define-public r-absseq (package (name "r-absseq") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ABSSeq" version)) (sha256 (base32 - "1ypd0wg3k2zzl0zf15c16dc38hfpsm5vv4x0x0yf90x0f8b6jpaz")))) + "1my2slp88qpb15qidjd646hlslvn8brv6i553h21c4c76jzxzsiz")))) (properties `((upstream-name . "ABSSeq"))) (build-system r-build-system) (propagated-inputs (list r-limma r-locfit)) @@ -2087,13 +2087,13 @@ ranking by fold-change and visualization.") (define-public r-adacgh2 (package (name "r-adacgh2") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADaCGH2" version)) (sha256 - (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd")))) + (base32 "1mmckrxhv23kl3g4d3n4hfdm97sfg2k36khzy9i6d73g7c033hsv")))) (properties `((upstream-name . "ADaCGH2"))) (build-system r-build-system) (arguments @@ -2129,13 +2129,13 @@ storing data.") (define-public r-adam (package (name "r-adam") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAM" version)) (sha256 (base32 - "1s1mzjxqld8gllfh6z9kg30klb4y1jrkrif7vwr18c0mhamf47a6")))) + "1hy7xdf6v2fqggvc9rdl90gn0l6vfbmvb23c61i8q45s3qsaxksp")))) (properties `((upstream-name . "ADAM"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -2164,13 +2164,13 @@ functionally associated genes} (GFAG).") (define-public r-adamgui (package (name "r-adamgui") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADAMgui" version)) (sha256 (base32 - "1ks799kgdmlxn5iyj6rzj04cm28klivclz3bg6bc4wad2q7h4ra9")))) + "0jc0sbmmc98z75x73ns3qwcvklvx73wqla87cki8sls6ywa8w93j")))) (properties `((upstream-name . "ADAMgui"))) (build-system r-build-system) (propagated-inputs @@ -2212,13 +2212,13 @@ the @code{GFAGpathUi} function.") (define-public r-adimpute (package (name "r-adimpute") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ADImpute" version)) (sha256 (base32 - "0wrprxd91vi4wwh9wixhx1ppbjsb56r4kcxgqz8w6ahr3z2387im")))) + "0a3r4bkf6g28lgsq21077ag9ba6zrfv6yflawx9fg73zdx4266jp")))) (properties `((upstream-name . "ADImpute"))) (build-system r-build-system) (propagated-inputs @@ -2261,13 +2261,13 @@ results from different methods into an ensemble.") (define-public r-adsplit (package (name "r-adsplit") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adSplit" version)) (sha256 (base32 - "0a05j1g42wnw5lcn6g6vp2z3mnjz185b2hvdg362ln270r19gch6")))) + "0nbdcrc2wiq3mkpayjslz66ik2vk3h3f18zg6df9xaivanxrkk5z")))) (properties `((upstream-name . "adSplit"))) (build-system r-build-system) (propagated-inputs @@ -2289,13 +2289,13 @@ the supporting gene set is determined.") (define-public r-affixcan (package (name "r-affixcan") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffiXcan" version)) (sha256 (base32 - "1jsdl477qhsq3rpqvgdm7navr4izpppfkiw0fvlhxwspgp3fjs6c")))) + "0nf5dkidar6zp5rvpd7i19gdb7mnam9rmca3z3anxi0pdnalwc9d")))) (properties `((upstream-name . "AffiXcan"))) (build-system r-build-system) (propagated-inputs @@ -2317,13 +2317,13 @@ expression values are known.") (define-public r-affyilm (package (name "r-affyilm") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyILM" version)) (sha256 - (base32 "0i2hjaqjz06ym5kbw5da1h3cahc630mjwljsji1l2ks0gjcipll0")))) + (base32 "02g0bg21ms0gmq6dvdcj91b0p47ppqcfvgj73y0mbdx6prrmcagx")))) (properties `((upstream-name . "affyILM"))) (build-system r-build-system) (propagated-inputs @@ -2344,13 +2344,13 @@ concentrations on behal of the Langmuir model.") (define-public r-affylmgui (package (name "r-affylmgui") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affylmGUI" version)) (sha256 - (base32 "0jds73pxqf522wcg8qd4b4k1qbhn51av5md1nhgcdnb6is0lzvxi")))) + (base32 "1m1gvz313h4x080889b05fjq60wn57dxlgq03qkwy65scl3x2fcn")))) (properties `((upstream-name . "affylmGUI"))) (build-system r-build-system) (propagated-inputs @@ -2376,13 +2376,13 @@ limma packages.") (define-public r-affyplm (package (name "r-affyplm") - (version "1.74.2") + (version "1.76.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affyPLM" version)) (sha256 - (base32 "0f0faxjzlg0znhjfvf1490yc54npkx659jx76cddm5hk7q0blv3v")))) + (base32 "1660nn4541f2k5qpzxkkkf9h92ndzqr0j1jpzh4czs466766kn8y")))) (properties `((upstream-name . "affyPLM"))) (build-system r-build-system) (inputs (list zlib)) @@ -2407,13 +2407,13 @@ also provided.") (define-public r-affyrnadegradation (package (name "r-affyrnadegradation") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AffyRNADegradation" version)) (sha256 (base32 - "1n6x2c0h6xmcll7mxq4n1y8ahqfmba8ppdcrjk9hf3nh5wngprkz")))) + "14s3kvxcc3qj931bf5ya088flijmn5z89hps3di98kkdsl3w6d4g")))) (properties `((upstream-name . "AffyRNADegradation"))) (build-system r-build-system) (propagated-inputs (list r-affy)) @@ -2432,13 +2432,13 @@ of samples that are affected by RNA degradation.") (define-public r-agdex (package (name "r-agdex") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AGDEX" version)) (sha256 (base32 - "0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8")))) + "0p9qmwhi4ik24m51cvgxnny4yfqv4v0rvra16bj5d3w9bw9yf3an")))) (properties `((upstream-name . "AGDEX"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-gseabase)) @@ -2459,13 +2459,13 @@ experiment.") (define-public r-aggregatebiovar (package (name "r-aggregatebiovar") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aggregateBioVar" version)) (sha256 (base32 - "1snsc2430cc7cd0k01n1rwa6vympd79g1mcch0paxxkq7msvfn42")))) + "0g7n6dj1scad833y2182946hn3yh4jad20wvw9ic8gmqb438vihj")))) (properties `((upstream-name . "aggregateBioVar"))) (build-system r-build-system) (propagated-inputs @@ -2493,13 +2493,13 @@ bulk RNA-seq tools.") (define-public r-agilp (package (name "r-agilp") - (version "3.30.0") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "agilp" version)) (sha256 (base32 - "15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0")))) + "0rm646iqc8hf8vfk0pdg064hm9k4k371bp1q4k7z2l16zhs8a07r")))) (properties `((upstream-name . "agilp"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/agilp") @@ -2515,13 +2515,13 @@ but which also provides utilities which may be useful for other platforms.") (define-public r-adductomicsr (package (name "r-adductomicsr") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "adductomicsR" version)) (sha256 (base32 - "0h180k4r1lrij1smpibbqgiki1hb2q87n5ay6habig4bxzbx773x")))) + "17cm65n2awbwmk5i8h1n30abk6pww42ngcy9m24dxz1qdbnvx5fn")))) (properties `((upstream-name . "adductomicsR"))) (build-system r-build-system) (propagated-inputs @@ -2560,13 +2560,13 @@ mass spectrometry} (MS1) data.") (define-public r-agimicrorna (package (name "r-agimicrorna") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AgiMicroRna" version)) (sha256 (base32 - "0q3hynyd4dhhh1a2b27y3rrshgvxfwv17k7yabh6g4pc12c33mf7")))) + "1gydc2sy0lf2h83dzr60w9k3ipqd8h62q6764xpn31girwx70rdz")))) (properties `((upstream-name . "AgiMicroRna"))) (build-system r-build-system) (propagated-inputs @@ -2590,13 +2590,13 @@ objects are used so that other packages could be used as well.") (define-public r-aims (package (name "r-aims") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AIMS" version)) (sha256 (base32 - "1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1")))) + "1mbwv70ypkb3x086css94m89wq9pqzd23i7nar1844vbqpw3j83q")))) (properties `((upstream-name . "AIMS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-e1071)) @@ -2614,13 +2614,13 @@ well as on dataset of gene expression data.") (define-public r-airpart (package (name "r-airpart") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "airpart" version)) (sha256 (base32 - "07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl")))) + "024vcxf23irlysc8srqii3zqhhldpwdcj0i4zzhz18x3bdy9cbj0")))) (properties `((upstream-name . "airpart"))) (build-system r-build-system) (propagated-inputs @@ -2661,13 +2661,13 @@ datasets.") (define-public r-amountain (package (name "r-amountain") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMOUNTAIN" version)) (sha256 (base32 - "0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8")))) + "12ml67882lscv05np4m80fg9d48dwkaa6kx5cga6x19kdx6xs2cj")))) (properties `((upstream-name . "AMOUNTAIN"))) (build-system r-build-system) (inputs (list gsl)) @@ -2685,20 +2685,20 @@ in multi-layer WGCN using a continuous optimization approach.") (define-public r-amplican (package (name "r-amplican") - (version "1.20.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "amplican" version)) (sha256 (base32 - "1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij")))) + "1bws4awpjvswzj53zwn9x5ra76ngpqn2h8hlr6y0x7j9wwwqldc7")))) (properties `((upstream-name . "amplican"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-biocparallel r-biostrings - r-clustercrit + r-cluster r-data-table r-dplyr r-genomeinfodb @@ -2732,13 +2732,13 @@ problems.") (define-public r-amaretto (package (name "r-amaretto") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AMARETTO" version)) (sha256 (base32 - "06j75c4j71fkkw5s52nbzb3k084y2f4v4h3js9dgsxxrd6jkzfz9")))) + "1yp2npw9mdjy0wchbp0y1r1ifyy63hdz2y3y8cia9c76nfv4627f")))) (properties `((upstream-name . "AMARETTO"))) (build-system r-build-system) (propagated-inputs @@ -2784,13 +2784,13 @@ canonical cancer pathways.") (define-public r-anaquin (package (name "r-anaquin") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Anaquin" version)) (sha256 (base32 - "08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5")))) + "0f2xc0pm7ld72fnmqirr0q2a5xfh12cag6s2yysblslh9ajyzcmw")))) (properties `((upstream-name . "Anaquin"))) (build-system r-build-system) (propagated-inputs @@ -2814,13 +2814,13 @@ analysis, modelling, and visualization of spike-in controls.") (define-public r-ancombc (package (name "r-ancombc") - (version "2.0.2") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANCOMBC" version)) (sha256 (base32 - "0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5")))) + "1wfbi8xyh2pxpjdv2zhml2l1h8c7fyfl5wyici3nm3rcs00n7m9w")))) (properties `((upstream-name . "ANCOMBC"))) (build-system r-build-system) (propagated-inputs @@ -2867,13 +2867,13 @@ these biases and construct statistically consistent estimators.") (define-public r-animalcules (package (name "r-animalcules") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "animalcules" version)) (sha256 (base32 - "1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr")))) + "1z46lpd2zi3b88i27qm48wy4acb2xsjh63zgxhfx2y4bgvr29ni7")))) (properties `((upstream-name . "animalcules"))) (build-system r-build-system) (propagated-inputs @@ -2926,13 +2926,13 @@ to understand their data better and discover new insights.") (define-public r-annotationhubdata (package (name "r-annotationhubdata") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHubData" version)) (sha256 - (base32 "0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95")))) + (base32 "109gi5cs82j135q00wg9dfx0z5m9bs1kc7s246ym13ik43z0h3qq")))) (properties `((upstream-name . "AnnotationHubData"))) (build-system r-build-system) (arguments @@ -2977,13 +2977,13 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "1j7n8c47j3njd5rnlrj8bkn4q5z7jpm0c9rdq1mlwd2i1yy9fz9b")))) + "17c5l10s756yzg69wdlwir88g0hn6zd0pdsycfr31n9n29nq59wa")))) (properties `((upstream-name . "AnVIL"))) (build-system r-build-system) (propagated-inputs @@ -3018,13 +3018,13 @@ to transform JSON responses to formats more amenable to manipulation in R.") (define-public r-aldex2 (package (name "r-aldex2") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ALDEx2" version)) (sha256 (base32 - "0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf")))) + "0gdkc8qwx3vpk5i09znlfrag7gk87piz61z90k96v6bm6x8sclb8")))) (properties `((upstream-name . "ALDEx2"))) (build-system r-build-system) (propagated-inputs @@ -3059,13 +3059,13 @@ paired or unpaired study designs.") (define-public r-alevinqc (package (name "r-alevinqc") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alevinQC" version)) (sha256 (base32 - "0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2")))) + "014jxp2ymxiywp2qa1b9f7iszgf95v03h9kgk8ljabnbia1zsl67")))) (properties `((upstream-name . "alevinQC"))) (build-system r-build-system) (propagated-inputs @@ -3093,13 +3093,13 @@ generated as HTML or PDF files, or as Shiny applications.") (define-public r-alphabeta (package (name "r-alphabeta") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlphaBeta" version)) (sha256 (base32 - "000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b")))) + "11431d453xszzjyxr10npnblhlrfw8hl5jgabpxla7cj77w02wnr")))) (properties `((upstream-name . "AlphaBeta"))) (build-system r-build-system) (propagated-inputs @@ -3132,13 +3132,13 @@ plants. The method has been specifically designed to: (define-public r-alpine (package (name "r-alpine") - (version "1.24.0") + (version "1.25.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alpine" version)) (sha256 (base32 - "0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0")))) + "01y467qcjl40fq0m9vq6fpyi5f243v4g67dnn5ddqwrzrkyb0j2r")))) (properties `((upstream-name . "alpine"))) (build-system r-build-system) (propagated-inputs @@ -3173,13 +3173,13 @@ data.") (define-public r-alpsnmr (package (name "r-alpsnmr") - (version "4.0.4") + (version "4.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AlpsNMR" version)) (sha256 (base32 - "19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv")))) + "0rp82y7163pjbl7n6fyywh4l0sgzn1z8kp83v0kg7xk3810mj9sm")))) (properties `((upstream-name . "AlpsNMR"))) (build-system r-build-system) (propagated-inputs @@ -3227,13 +3227,13 @@ data. Efficient plotting with 1-D data is also available. Basic reading of (define-public r-altcdfenvs (package (name "r-altcdfenvs") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "altcdfenvs" version)) (sha256 (base32 - "0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0")))) + "1jpimj195rdw86pp623ylrmcxkxmn8qmc84vsw9prnf3gdz3q18b")))) (properties `((upstream-name . "altcdfenvs"))) (build-system r-build-system) (propagated-inputs @@ -3258,13 +3258,13 @@ create an alternative mapping from sequences.") (define-public r-aneufinder (package (name "r-aneufinder") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AneuFinder" version)) (sha256 (base32 - "154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00")))) + "1l33yb20pynkvlla1dmgbwjhnhxh067fci0ciryxmbzqwq2sn1kc")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3287,7 +3287,6 @@ create an alternative mapping from sequences.") r-reshape2 r-ggdendro r-ggrepel - r-reordercluster r-mclust r-cowplot)) (home-page "https://bioconductor.org/packages/AneuFinder/") @@ -3300,13 +3299,13 @@ sequencing data.") (define-public r-anf (package (name "r-anf") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ANF" version)) (sha256 (base32 - "0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j")))) + "08vkkfccfq8j4hanxsmjx5657kkw4qcp46qfhqvp1sd6wym69wzw")))) (properties `((upstream-name . "ANF"))) (build-system r-build-system) (propagated-inputs @@ -3328,13 +3327,13 @@ network fusion.") (define-public r-annmap (package (name "r-annmap") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annmap" version)) (sha256 (base32 - "18ia189qgsbcivpfsfss05dnd3kdc6gmswq8i1whwf9n227b2cv3")))) + "0gilb8yxba1cqi678w9xkq77m8lf3k8dqcldh68cll61xsgihl1v")))) (properties `((upstream-name . "annmap"))) (build-system r-build-system) (propagated-inputs @@ -3362,13 +3361,13 @@ Functions to plot gene architecture and BAM file data are also provided.") (define-public r-antiprofiles (package (name "r-antiprofiles") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "antiProfiles" version)) (sha256 (base32 - "0f32373ncfjbvy05yngmfhhdgyc99a4idz3ry2xlabdmrbs5yac3")))) + "0ix0r36fs6vr0gyryi1j15pcc0hvpynsg9505w95dsn3p4fdnhg8")))) (properties `((upstream-name . "antiProfiles"))) (build-system r-build-system) (propagated-inputs @@ -3388,20 +3387,22 @@ tumor samples from healthy controls.") (define-public r-arrayexpress (package (name "r-arrayexpress") - (version "1.57.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ArrayExpress" version)) (sha256 (base32 - "1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6")))) + "1ib33fw379sakk084csa3pwcc3wvba38ily6mmv2ax1wh16i0pfz")))) (properties `((upstream-name . "ArrayExpress"))) (build-system r-build-system) (propagated-inputs (list r-biobase + r-httr + r-jsonlite r-limma r-oligo - r-xml)) + r-rlang)) (home-page "https://bioconductor.org/packages/ArrayExpress") (synopsis "Building R objects from ArrayExpress datasets") (description @@ -3413,13 +3414,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.") (define-public r-asafe (package (name "r-asafe") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASAFE" version)) (sha256 (base32 - "1q4i33rw1qb8bnvkl06izl4nyl9lzgwy8rwrmvbrz1c384pmy8yj")))) + "05xw42552x7by63psb05hvjraax66flg94i331ca61zx107q7fai")))) (properties `((upstream-name . "ASAFE"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -3436,13 +3437,13 @@ pairs.") (define-public r-aseb (package (name "r-aseb") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASEB" version)) (sha256 (base32 - "1kr6l2ma7wzy8i9dn86zx927yvx1l4bnkxhv97ra3sh5vr6m8ywa")))) + "1dq6b5rg9iw6hdjmd7g0w64z7cxm52yg1cjyv355qs064dx26nph")))) (properties `((upstream-name . "ASEB"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/ASEB") @@ -3463,13 +3464,13 @@ RNAs.") (define-public r-asgsca (package (name "r-asgsca") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASGSCA" version)) (sha256 (base32 - "12wap8xbq6xl7p430yd9yy5kdhs15n7nmv2h3k9bsi0f4m6md02i")))) + "0vb37rvrb08qvv0i2k9jnqpajzpj044ww05w3kq1kypbby0c84zs")))) (properties `((upstream-name . "ASGSCA"))) (build-system r-build-system) (propagated-inputs (list r-mass r-matrix)) @@ -3486,13 +3487,13 @@ model as latent variables.") (define-public r-asics (package (name "r-asics") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASICS" version)) (sha256 (base32 - "0c2b3gdza58vqhharhw8967p2w2knnrm5s2svvnnjbf67qbg45b7")))) + "0svl9wnfn9z88j1yyl30b1f3d14h01x4cga8q04x530723xnjws7")))) (properties `((upstream-name . "ASICS"))) (build-system r-build-system) (propagated-inputs @@ -3520,13 +3521,13 @@ the spectra of the library with a sparse penalty.") (define-public r-aspli (package (name "r-aspli") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASpli" version)) (sha256 (base32 - "0gwp5ijpxjy6hd1090cmwbfrfac1qqrzxc06n1j89c0va7wm9l4k")))) + "0462hf7anpmmqq4585kmjilw1q229r38lijbxq8xg0f3m8xvr1ga")))) (properties `((upstream-name . "ASpli"))) (build-system r-build-system) (propagated-inputs @@ -3568,13 +3569,13 @@ that might arise in splicing patterns.") (define-public r-assessorf (package (name "r-assessorf") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AssessORF" version)) (sha256 (base32 - "125qkjsjyxp6zk3nzfamakyfgm7wd7w9vv1vn7xyyylpqpa8rpml")))) + "16nv6sh7z3l6ff3a7zrixkc04mhrak38q045xlirgljkcragz1c5")))) (properties `((upstream-name . "AssessORF"))) (build-system r-build-system) (propagated-inputs @@ -3597,13 +3598,13 @@ start codons as the forms of evidence.") (define-public r-asset (package (name "r-asset") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ASSET" version)) (sha256 (base32 - "13zwnjap4y0s3qqv10mv2i4mqan9nmkm2l29i448h1j3wwfq18j2")))) + "1vksbfd4wd2xcc0nl3wp53vm0jyqy97p0hqps2aml04745vkg023")))) (properties `((upstream-name . "ASSET"))) (build-system r-build-system) (propagated-inputs (list r-mass r-msm r-rmeta)) @@ -3624,13 +3625,13 @@ variant.") (define-public r-atena (package (name "r-atena") - (version "1.4.1") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atena" version)) (sha256 (base32 - "0j6jq1cll8440i2srmy4lbvvyqawailk9byl9bnnzln1mdgys8r7")))) + "1057mkxrjfnqhb1mydhd7vlb1s8h7n4zc4cl063gw4sgj6mw99ij")))) (properties `((upstream-name . "atena"))) (build-system r-build-system) (propagated-inputs @@ -3645,7 +3646,6 @@ variant.") r-matrixstats r-rsamtools r-s4vectors - r-scales r-sparsematrixstats r-squarem r-summarizedexperiment)) @@ -3666,13 +3666,13 @@ transcripts in an integrated manner.") (define-public r-atsnp (package (name "r-atsnp") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "atSNP" version)) (sha256 (base32 - "12za1agpbjjg4i94mikbkdbwqnkzzwz07v0gwdc7lpa9899q2ycb")))) + "14j8lbry4wpn8izch1nra5npg4qsh49ql4bf21jvvr3gl3qa1g7l")))) (properties `((upstream-name . "atSNP"))) (build-system r-build-system) (propagated-inputs @@ -3699,13 +3699,13 @@ SNP-led changes in motif matches.") (define-public r-attract (package (name "r-attract") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "attract" version)) (sha256 (base32 - "0r5vykjqq33gchqv0wp2i6wpnk95cv26w5j4yqxcnw0bnqfhrgkm")))) + "1lb6npxm5f82z8278v6fh7k5w8d4z73881iplm3ashc27wiw6sz3")))) (properties `((upstream-name . "attract"))) (build-system r-build-system) (propagated-inputs @@ -3730,13 +3730,13 @@ transcriptionally-coordinated changes in gene expression.") (define-public r-awfisher (package (name "r-awfisher") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AWFisher" version)) (sha256 (base32 - "1psbxxrwb6mk2jwjw963vwdczb3i5590rcm7hk43kpiw45i1q1j9")))) + "1c6rr1z1rhvn8w1kb3nnjlfacfr22vwm1rsa1xqm2hmghs01bq4x")))) (properties `((upstream-name . "AWFisher"))) (build-system r-build-system) (propagated-inputs @@ -3754,13 +3754,13 @@ meta-pattern.") (define-public r-awst (package (name "r-awst") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "awst" version)) (sha256 (base32 - "0dvzkqpjv7whns9q8zj6n2nyvnaw2ib7i53vf049n94x52vh9x15")))) + "0nwpfxfrx9rw4vl02vr311ivmmk96ajlwyhwms642hjv74j2yiji")))) (properties `((upstream-name . "awst"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -3781,13 +3781,13 @@ artifacts.") (define-public r-baalchip (package (name "r-baalchip") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaalChIP" version)) (sha256 (base32 - "16s67v6mkv14dkk1r7c50brm7198b84h87h1wrahmrrcnzq8pi0n")))) + "0bp8p7cn59iv08cf4yw9xl1f83dcr6v1kqvggxjals8y4gmls9nz")))) (properties `((upstream-name . "BaalChIP"))) (build-system r-build-system) (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl @@ -3821,13 +3821,13 @@ alleles, a known phenotypical feature of cancer samples.") (define-public r-basespacer (package (name "r-basespacer") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BaseSpaceR" version)) (sha256 (base32 - "07pqs0jkwcbxavc65sanvhvzc9spkk46bqnwz162f3pvrz15b5h7")))) + "15aqf2s51gl6gcnv24170v9hlq1vgya58qh1f5vjmark7j2k8vvm")))) (properties `((upstream-name . "BaseSpaceR"))) (build-system r-build-system) (propagated-inputs (list r-rcurl r-rjsonio)) @@ -3868,13 +3868,13 @@ you will have to normalize your data beforehand.") (define-public r-bader (package (name "r-bader") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BADER" version)) (sha256 (base32 - "1hkvmfik4m2yw5xg4k2g551l27i64blbsdvp1kmvvyix66p53hsr")))) + "0g3yvgrarpdcxpvjrxg0gbdcagknh80cr0xyzinzpmiiz0rywmzc")))) (properties `((upstream-name . "BADER"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BADER") @@ -3892,13 +3892,13 @@ can be used for further down-stream analyses such as gene set enrichment.") (define-public r-badregionfinder (package (name "r-badregionfinder") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BadRegionFinder" version)) (sha256 (base32 - "0bsgdjchwsfc8aiwiacr454kw97dbymq6v450m1fx7hxmmpqz1sm")))) + "04bzb3i461gwkq9ygkjljpjk32c3arqr08hfzxyig1sarrryzl3q")))) (properties `((upstream-name . "BadRegionFinder"))) (build-system r-build-system) (propagated-inputs @@ -3919,13 +3919,13 @@ Various visual and textual types of output are available.") (define-public r-bambu (package (name "r-bambu") - (version "3.0.8") + (version "3.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "072rys45f9nl4b2dq559qakjcp2990ncdw49j49761izxgc7byzs")))) + "0vmfynsyl1bdkbaxp278sgs52kmixi8kzzjck69arbnvmg0wp9ib")))) (properties `((upstream-name . "bambu"))) (build-system r-build-system) (propagated-inputs @@ -3962,13 +3962,13 @@ usage.") (define-public r-bandits (package (name "r-bandits") - (version "1.14.2") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BANDITS" version)) (sha256 (base32 - "11w0azh2g0y331imqpllnb0csjxf3gs1767cc67c1zp0ykg6yq8l")))) + "04l6iy0sij7zhzswhxjzir3xmrjnp6aapp0a93xp01xiv2sgdzni")))) (properties `((upstream-name . "BANDITS"))) (build-system r-build-system) (propagated-inputs @@ -4000,13 +4000,13 @@ the posterior densities for the average relative abundance of transcripts.") (define-public r-banocc (package (name "r-banocc") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "banocc" version)) (sha256 (base32 - "0d7ss3df6zcfsh8kgy35ghxa6f27ynjhdbi6mdypgk9q24f64r78")))) + "0yi70y87isb34jc1wrnz4gr0d0f2zw44555s50j3qdnj1x8cld9y")))) (properties `((upstream-name . "banocc"))) (build-system r-build-system) (propagated-inputs @@ -4028,13 +4028,13 @@ estimates for each correlation element.") (define-public r-barcodetrackr (package (name "r-barcodetrackr") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "barcodetrackR" version)) (sha256 (base32 - "1b3z83nkl8csxs88rcbmkkfjps71mwnylvpy3kjzyi02xw0kh0c1")))) + "155lxqqq2mgrz9i04xvv8y7gh2iacw6qd3mzijzbvrbm605qb3p8")))) (properties `((upstream-name . "barcodetrackR"))) (build-system r-build-system) (propagated-inputs @@ -4070,14 +4070,14 @@ retrieval analyses, or similar technologies.") (define-public r-biocversion (package (name "r-biocversion") - (version "3.16.0") + (version "3.17.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocVersion" version)) (sha256 (base32 - "1djp23y131dyx4g22f9r7an177bq0mky94bvpqvc8b14166g0ynw")))) + "0n29adnb62agp9li8rmn68z653d2m41iy9zjz75h43a05drlgp33")))) (properties `((upstream-name . "BiocVersion"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BiocVersion/") @@ -4090,13 +4090,13 @@ of Bioconductor.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.44.0") + (version "0.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "17dhr7vaph8dnvyklszyas7y8i64mxqxhnfhb6q3l47gq5if8645")))) + "19kwpis282i8x31xlh8nc3z6vvn23p3wpx7wmrqhclf8ymq61c7z")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -4110,13 +4110,13 @@ packages.") (define-public r-breakpointr (package (name "r-breakpointr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "breakpointR" version)) (sha256 (base32 - "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx")))) + "001n99lilymgqxmpi4v89gw60j1mx13rvppv1ff1pbnk1zcmg53n")))) (properties `((upstream-name . "breakpointR"))) (build-system r-build-system) (propagated-inputs @@ -4144,13 +4144,13 @@ export of Strand-seq data.") (define-public r-cardelino (package (name "r-cardelino") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cardelino" version)) (sha256 (base32 - "1ma4clkrkrjvy12ln2d2smyzzsz9y9554f5wgwmh9kv6s4xc66qs")))) + "0ivhqd3da23iy2qklk2nljkjjr943m9r2y1q51fphld33izmv64v")))) (properties `((upstream-name . "cardelino"))) (build-system r-build-system) (propagated-inputs (list r-combinat @@ -4182,13 +4182,13 @@ stochastic dropout events as well as systematic allelic imbalance is used.") (define-public r-coverageview (package (name "r-coverageview") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CoverageView" version)) (sha256 (base32 - "0cqvwp0ybxgnk9kif3ly780v23pwv4cyh46kk47gxcxqqkjv36ld")))) + "1ci07y75nvvv1mxy23v6jp5xb6n023fvlqh9il5lsdqwyfl5nz9s")))) (build-system r-build-system) (propagated-inputs (list r-s4vectors @@ -4209,13 +4209,13 @@ how the coverage distributed across the genome.") (define-public r-cummerbund (package (name "r-cummerbund") - (version "2.40.0") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cummeRbund" version)) (sha256 (base32 - "1fzkhnlgv4zd0slr12d5aichyxsca86p82fyjymiz7f5fqdvqmd9")))) + "1xin1azby96xxp4yyd4wc3rfcjc2g9p01ksfd89bk2vxcclccqxn")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -4239,13 +4239,13 @@ used visualizations.") (define-public r-dama (package (name "r-dama") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "daMA" version)) (sha256 (base32 - "062nxfry9w674ja3q9zs4df2hvf4wws9jdqpy84g6nb0309vbhqf")))) + "0z4y57hna312pkhkchair8calm7wl40rx8lcm8i6h1789hba063d")))) (properties `((upstream-name . "daMA"))) (build-system r-build-system) (propagated-inputs (list r-mass)) @@ -4261,13 +4261,13 @@ factorial microarray data.") (define-public r-damefinder (package (name "r-damefinder") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DAMEfinder" version)) (sha256 (base32 - "1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1")))) + "0m8g1sp55mxa0qswpqkzk73myhhy3s49c21hf97sk0lxis5lagcd")))) (properties `((upstream-name . "DAMEfinder"))) (build-system r-build-system) (propagated-inputs @@ -4302,14 +4302,14 @@ offers nice visualization of methyl-circle plots.") (define-public r-dearseq (package (name "r-dearseq") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "1f9hz4jp862jm1grf4qzdvnzp17ri0n1rhfafgkc1j73z6whw1b0")))) + "023kychm361z4zxyq9rmbx44p2nf7ysq2anlhn0q257v0bkwxn9i")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -4341,16 +4341,53 @@ set analyses, and can deal with repeated or longitudinal data.") (define-public r-debcam (package (name "r-debcam") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "debCAM" version)) (sha256 (base32 - "09dm861adbxdy3ncfdxq46wjr4hpn56c66n64xm9gwzkzsrxyc2a")))) + "11vqfkyd3fklc8fhn850kklph8x4pmwclb9xbqji4i21222m89hh")) + (snippet + '(for-each delete-file + '("inst/java/CornerDetect.jar" + "inst/java/lib/pj20150107.jar"))))) (properties `((upstream-name . "debCAM"))) (build-system r-build-system) - (inputs (list openjdk)) + (arguments + (list + ;; XXX: since the upgrade to R 4.3.0 this package takes too long to be + ;; loaded. + #:tests? #false + #:configure-flags '(list "--fake") + #:modules + '((guix build r-build-system) + ((guix build ant-build-system) #:prefix ant:) + (guix build utils)) + #:imported-modules + `((guix build ant-build-system) + ,@%r-build-system-modules) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'build-jar + (lambda* (#:key inputs #:allow-other-keys) + (install-file + (search-input-file inputs "/share/java/pj20150107.jar") + "inst/java/lib") + (with-directory-excursion "java" + (mkdir "build") + (invoke "javac" "-d" "./build" + "-cp" "../inst/java/lib/pj20150107.jar" + "CornerDetectTopN.java" + "FixSizedPriorityQueue.java") + (with-directory-excursion "build" + (apply invoke "jar" "cvf" "../../inst/java/CornerDetect.jar" + (find-files ".")))))) + (add-after 'install 'strip-jar-timestamps + (assoc-ref ant:%standard-phases 'strip-jar-timestamps))))) + (inputs + (list (list icedtea "jdk") + java-pj)) (propagated-inputs (list r-apcluster r-biobase @@ -4363,7 +4400,8 @@ set analyses, and can deal with repeated or longitudinal data.") r-pcapp r-rjava r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs + (list r-knitr zip)) (home-page "https://bioconductor.org/packages/debCAM") (synopsis "Deconvolution by convex analysis of mixtures") (description @@ -4380,13 +4418,13 @@ knowledge can achieve semi-supervised deconvolution of mixtures.") (define-public r-decipher (package (name "r-decipher") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DECIPHER" version)) (sha256 (base32 - "01hzxd5f5v2kspx5jd7l21bn87cfgm9aah3zd4d6kyxv98h5a3n1")))) + "16z6yk8rr2115z6g1l7fl01binxm29vnxsnsm2wzfvc5vv49927n")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -4479,13 +4517,13 @@ mechanism based on the shared signatures.") (define-public r-decomptumor2sig (package (name "r-decomptumor2sig") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decompTumor2Sig" version)) (sha256 (base32 - "0agvmgwyk458lhhhspd8243n4897f0q7jf9yqhwsl5wi8011vmqd")))) + "028sczy1d108i05ymr1wpj6jdrcds476wbmmc7rzzflzyg4aix75")))) (properties `((upstream-name . "decompTumor2Sig"))) (build-system r-build-system) (inputs (list perl)) ;script/extractSpecColumns.pl @@ -4522,13 +4560,13 @@ of the signatures to the mutation load of the tumor.") (define-public r-deconrnaseq (package (name "r-deconrnaseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DeconRNASeq" version)) (sha256 (base32 - "05rwqchfspy8i9fcj9526rl5vvk0rrgr95nvxzdj0sa2136my8y4")))) + "0bmkyci31p7g097i8fvc0s1fz47hv6vp5rcfqqkvclm86wfkkmkc")))) (properties `((upstream-name . "DeconRNASeq"))) (build-system r-build-system) (propagated-inputs @@ -4549,13 +4587,13 @@ single expression profiles.") (define-public r-decontam (package (name "r-decontam") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decontam" version)) (sha256 (base32 - "0bk7ia2flnxwa99b8mf3xdvap3xqa4pvpsrgbnyapxbaqxr5zf82")))) + "08niwixy4m6gqmazisxzbbla9nsxicpa685jy3r6knapwaznvcb2")))) (properties `((upstream-name . "decontam"))) (build-system r-build-system) (propagated-inputs @@ -4575,13 +4613,13 @@ negative control samples.") (define-public r-deconvr (package (name "r-deconvr") - (version "1.4.3") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deconvR" version)) (sha256 (base32 - "1jz7q4rv3m85bcvarjhqsyc2330fynb0wr5ajd2qffznczk846xb")))) + "1r5js5prwy1libnf1g1a4pdi15pj216bb8ajhzii3symn5r0cdj9")))) (properties `((upstream-name . "deconvR"))) (build-system r-build-system) (propagated-inputs @@ -4620,13 +4658,13 @@ make mapping WGBS data to their probe IDs easier.") (define-public r-decoupler (package (name "r-decoupler") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "decoupleR" version)) (sha256 - (base32 "1872pi2v9gymdpqdhab10ash4b2w8sbk1p635lf0p6s4679syhdi")))) + (base32 "012d76jwgg6fwfjc00zdws59y6jbj0grzd4lgjrqs2afp2ycmh9s")))) (properties `((upstream-name . "decoupleR"))) (build-system r-build-system) (propagated-inputs @@ -4661,13 +4699,13 @@ targeted by a kinase.") (define-public r-deepsnv (package (name "r-deepsnv") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "deepSNV" version)) (sha256 (base32 - "051xcg9lx8plbfhiacrv1wsxfac0qqspysq960ppibkf4m8crk81")))) + "11cnyy3hyn8akhmax25293mx2blcs8ba5vfax6mx6hjhb577hkwb")))) (properties `((upstream-name . "deepSNV"))) (build-system r-build-system) (propagated-inputs @@ -4697,19 +4735,23 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.24.0") + (version "0.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0nl1v0mxb759wiia2rsxay0cv0q631gqyzgaa10s175lhzsb8r6p")))) + "0zp49ksqcgy5bzlf63s8zc7flv2x66qkn02h49wmyj5ix20al0a7")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics r-s4vectors r-iranges r-matrix - r-matrixgenerics)) + (list r-biocgenerics + r-iranges + r-matrix + r-matrixgenerics + r-s4arrays + r-s4vectors)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/DelayedArray") @@ -4724,16 +4766,47 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), @code{Matrix} objects, and ordinary arrays and data frames.") (license license:artistic2.0))) +(define-public r-densvis + (package + (name "r-densvis") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "densvis" version)) + (sha256 + (base32 + "1291gp5wj9c47y291c1hqb12dj2zh6xrf0g38kllspqg9885cs54")))) + (properties `((upstream-name . "densvis"))) + (build-system r-build-system) + (propagated-inputs (list r-assertthat r-basilisk r-irlba r-rcpp + r-reticulate)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/densvis") + (synopsis + "Density-preserving data visualization via non-linear dimensionality reduction") + (description + "This package implements the density-preserving modification to t-SNE and +UMAP described by Narayan et al. (2020) <doi:10.1101/2020.05.12.077776>. +den-SNE and densMAP aim to enable more accurate visual interpretation of +high-dimensional datasets by producing lower-dimensional embeddings that +accurately represent the heterogeneity of the original high-dimensional space, +enabling the identification of homogeneous and heterogeneous cell states. +This accuracy is accomplished by including in the optimisation process a term +which considers the local density of points in the original high-dimensional +space. This can help to create visualisations that are more representative of +heterogeneity in the original high-dimensional space.") + (license license:expat))) + (define-public r-derfinderhelper (package (name "r-derfinderhelper") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "derfinderHelper" version)) (sha256 - (base32 "118rjmqy53viczdwj70kaszkpg2r2zbq60k49jg7fqb81prdwy04")))) + (base32 "0ww4lvwmm8rf44wgksg98bqh7zlm503c4gc8dwilb1w0dz2k7qll")))) (properties `((upstream-name . "derfinderHelper"))) (build-system r-build-system) (propagated-inputs @@ -4752,13 +4825,13 @@ calculation in parallel.") (define-public r-dmrcate (package (name "r-dmrcate") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DMRcate" version)) (sha256 (base32 - "0iphlsbam5fcxbj5j0cmqk3wz5ykwz0mvk3qbrhzxbpf2h4w2qib")))) + "1kcp0hgxnrcslphdqb25jsicif52r1sk8c7sn73jkdxy4n64idbm")))) (properties `((upstream-name . "DMRcate"))) (build-system r-build-system) (propagated-inputs @@ -4792,13 +4865,13 @@ possibly confounded by SNPs and cross-hybridisation. It includes (define-public r-drimseq (package (name "r-drimseq") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DRIMSeq" version)) (sha256 - (base32 "0cj3fyb99fh30f35ra1gpvzwplszbwvwk33ppgyh1zx2axsx164w")))) + (base32 "1i9lcp31g94mllkwcyfablj27qr8v7vqk9j96ywrdfpj8dmcrw98")))) (properties `((upstream-name . "DRIMSeq"))) (build-system r-build-system) (propagated-inputs @@ -4827,13 +4900,13 @@ results.") (define-public r-dss (package (name "r-dss") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DSS" version)) (sha256 (base32 - "1qm0pq6495fn2zrbddaadb1w01ry76rg8mmbmxf3zws9pww48jgf")))) + "1aslbzwqfp609ym98k6cjjf6r1ns9hxcpx4igfjhqf2v0pazz2q8")))) (properties `((upstream-name . "DSS"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocparallel r-bsseq)) @@ -4853,13 +4926,13 @@ Beta-Binomial distributions.") (define-public r-bluster (package (name "r-bluster") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bluster" version)) (sha256 (base32 - "1xi9vl09nm95l35kb9n3pn3j9qxw8976lss3cx0ppwnxd2mjr6vy")))) + "15f103lpl686730vl8g69fhki9iq2ncgr5dm6qm2xc9bq9vh65s9")))) (properties `((upstream-name . "bluster"))) (build-system r-build-system) (propagated-inputs @@ -4883,13 +4956,13 @@ and evaluate clustering results.") (define-public r-ideoviz (package (name "r-ideoviz") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IdeoViz" version)) (sha256 (base32 - "0jpj8bkfm3jcb5fj0xhh13vqh2dcgdgi4i1qk3wx1301irkk7fgf")))) + "1za1cxf734mar9hbvqrijdg61g0jag9jdzmi8p8ka62xbikxqa3s")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -4907,14 +4980,14 @@ arbitrary genomic intervals along chromosomal ideogram.") (define-public r-infercnv (package (name "r-infercnv") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "infercnv" version)) (sha256 (base32 - "04m51jdahhmj31cs2af9il5zijkpb255f9p06i8ga0v3g79gj1bp")))) + "19fk4pzhwj9pfh4vg943xb4cdfpq65ax75d61w1mm3f71gg56z5g")))) (properties `((upstream-name . "infercnv"))) (build-system r-build-system) (inputs (list python)) @@ -4967,13 +5040,13 @@ over-abundant or less-abundant as compared to that of normal cells.") (define-public r-iranges (package (name "r-iranges") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0jvavhl6p2di0n5176gg7shfmpg79rngl2gaw423icswdf8kay89")))) + "13kmh5zik3gw4jzh666zd3vmv915fcac5lx76s9q38x01m4gd7ld")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -4995,13 +5068,13 @@ possible.") (define-public r-isoformswitchanalyzer (package (name "r-isoformswitchanalyzer") - (version "1.20.0") + (version "1.21.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IsoformSwitchAnalyzeR" version)) (sha256 - (base32 "06kcx0a7xxzqhf4y8l69my5chh06sfahsaz6anhana7shym3yif5")))) + (base32 "1vzzsqjnkaffyxgvw6bsbxhgg1102cap2hsmzkhwzh6bvh02bwkx")))) (properties `((upstream-name . "IsoformSwitchAnalyzeR"))) (build-system r-build-system) (propagated-inputs @@ -5070,13 +5143,13 @@ AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).") (define-public r-italics (package (name "r-italics") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ITALICS" version)) (sha256 - (base32 "0g937h9zxkxnm424wh58b46mfasdd7pqy5c04r0a46mx9lxibgbs")))) + (base32 "09yia158mrv9r32iw88jlbfd6l7hzmglv8ni7i28x18qvnhp2a08")))) (properties `((upstream-name . "ITALICS"))) (build-system r-build-system) (propagated-inputs @@ -5250,14 +5323,14 @@ performing parallel computations on multicore machines.") (define-public r-affy (package (name "r-affy") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "1iix9mq4aph6avs2qr64a7hip461cif56k6npvs5g69nj3rn50gj")))) + "15hpxflygpy1sid0c4hlzmsc13nqyzs6j74md0ri478qysiqjnpf")))) (build-system r-build-system) (propagated-inputs (list r-affyio @@ -5278,14 +5351,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "18bxnjcl7cbgwm3yf58608ghwnpci94xgil11zmbpgzgrpv9pkrs")))) + "1bsav6d3dhn2fs7gjd1jvrb448ckxw5l6ikrdv63cdnnjk0dxl62")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -5344,14 +5417,14 @@ Command Console} (AGCC)-compatible sample annotation files.") (define-public r-affycontam (package (name "r-affycontam") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyContam" version)) (sha256 (base32 - "0phf9rvxr45zq9m5rcjsiixmj9ilz518l628l8cd1hzfdk240ffy")))) + "07a6kd51rlj433yxmyd2j8nl8qn1hw8wv3mk270dp8xxlk613y3p")))) (properties `((upstream-name . "affyContam"))) (build-system r-build-system) (propagated-inputs @@ -5367,14 +5440,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.") (define-public r-affycoretools (package (name "r-affycoretools") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affycoretools" version)) (sha256 (base32 - "17slls8dihjnpm6bynic8cm2fbnfl5iqwimz0wz7c9x44d1bxi4l")))) + "1h065fhw0n2ga74csyhqbj4qfhkg058pqa684ixcski4rhsd7hcf")))) (properties `((upstream-name . "affycoretools"))) (build-system r-build-system) (propagated-inputs @@ -5409,14 +5482,14 @@ to streamline the more common analyses that a Biostatistician might see.") (define-public r-affyio (package (name "r-affyio") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1bdcz9sz4khs7p4ddryc4ir0fwcjrkwqka8y0c9n36ykiv4myfib")))) + "1r1c0iwix0n8r433x4bv8hvzhkablc4xkdgg2b1fk4ijhd1iwf3c")))) (build-system r-build-system) (propagated-inputs (list r-zlibbioc)) @@ -5433,14 +5506,14 @@ CDF file formats.") (define-public r-affxparser (package (name "r-affxparser") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affxparser" version)) (sha256 (base32 - "0p42rpyh96aph9jr8kiyjvv860jn7m7ji2nrib2vr2nl0jyaxqjs")))) + "0n86my3bzy3g7xn60kizs5ym5m016zrkg7dv96kx246mrnv0ax8y")))) (properties `((upstream-name . "affxparser"))) (build-system r-build-system) (home-page "https://github.com/HenrikBengtsson/affxparser") @@ -5461,14 +5534,14 @@ structure.") (define-public r-annotate (package (name "r-annotate") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "06jmnv36y3n6pl1vs6mp14sgyzl4l37g13diaa49k7qwp1kdpl3a")))) + "1104r6jdy3nza8329xmq428ljfbfi2xwkd92sw519g0yqryh09vy")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -5488,13 +5561,13 @@ microarrays.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.60.2") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg")))) + "0a5brfd010p0ks8b7kvrynirmzv3p74r9vqwv5wyz4kbnasfd1v1")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -5518,13 +5591,13 @@ annotation data packages using SQLite data storage.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk")))) + "10jkxjmsshrr08c397qvkgrcfwzvrbd2hci1nal4vd5mm77f9cl9")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -5543,14 +5616,14 @@ used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.40.2") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "1ab7nl9zrlhlkwjrjr69zqq5hy9a8rp457hcr075n8qm5r5lf6wd")))) + "0s1k32li3nygg01nv9hbs7n6pabaassxmm4z5jggp6apdzkjpsc7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5575,14 +5648,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n")))) + "0ri8qj5j10bhprkb810c2hl5sl944kpb8rf5lab6nxykzgyz73v0")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -5616,14 +5689,14 @@ by the user, helping with quick and reproducible access.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.28.0") + (version "3.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "01g9vfkmpfkn9nv71jyybq93lid6x93jbadjahngy98w67n3sin4")))) + "118yqvbj4ad2b2bik0zi3ir15kxh9fbdi9qqyk52isvcdbv6069p")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -5640,14 +5713,14 @@ classes.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "059pkm5pg9ssd0l8xrm13d0hscqnmlqcb4qb5p4fbzgx6088zg05")))) + "18058j3fc47qcwvzgpb8mbc7cd1pywzrz3a36iqz93ihzjmymydk")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -5670,18 +5743,19 @@ paired-end data.") (define-public r-biobase (package (name "r-biobase") - (version "2.58.0") + (version "2.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "0rp541nphbcya6kbk1nzrrb05g5m6pxb3yqz5cj873di9vsqlyfv")))) + "1xjs5nxr3dffllp599hf0cx71a2czqmhf7zj2sp6rz06kcxib905")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/Biobase") (synopsis "Base functions for Bioconductor") (description @@ -5692,13 +5766,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.54.1") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "13nhp97cklaimc3cd931hz584nc58szk2gyxrkfhp7knfli6jbpi")))) + "10cjysqnc1wr0ld3wjl79zv0irrmxb8hf03y63fbwcc43rjcgv07")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -5732,13 +5806,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biomartr (package (name "r-biomartr") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (cran-uri "biomartr" version)) (sha256 (base32 - "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz")))) + "093v32r6s9sn7yisa4fdwgjif313ap19nvq0sbsgj2482k646d55")))) (properties `((upstream-name . "biomartr"))) (build-system r-build-system) (propagated-inputs @@ -5777,13 +5851,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.32.6") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1aq3b5fjs8j0d6nf3992a6gnzvmmaxbbkrj1im0k6ppsqac6dlj0")))) + "14ddzx7c5d4c599zwfx03bz3bqvxfc748znk929g3200brggqkqd")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -5828,13 +5902,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1z86s8ncl91pxcjnv8fwvgwjjnd384dn5paylwyymrigph4ca4kk")))) + "0gcx07d1qbrhkw30gfg39ln9jm71bya9f7si142lzs3p3bask8a2")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -5856,14 +5930,14 @@ biological sequences or sets of sequences.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0k56bq3g5vwnd0vkqg7x7v7i9bakwb8s1yl7k5nwj26k4aw96lw6")))) + "0na37f2nfavgxd2xhprfb6bv68zm2h6glbkffspc3gsnw1q5h6da")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -5898,13 +5972,13 @@ effort and encourages consistency.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.66.3") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1ps7s6i9mv8ys8k2xw8fdkh2rl2n3kcf2q4zsz6kcz5qpav95ys6")))) + "0fx2mkzyhbn8iayw14nr913wd4xhp76b1zjb85akrxaab2dm4zz8")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -5929,14 +6003,14 @@ genome data packages and support for efficient SNP representation.") (define-public r-category (package (name "r-category") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1j62b3ycvb27p80k1a1qj4pdf8cjynf5fkj65v74c3l1hgl9qxnh")))) + "1wjf6xbnys7nv8z4xrzck1wk5xifkdni672kigs0aqdxqj8d80f5")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -5960,13 +6034,13 @@ analysis.") (define-public r-champ (package (name "r-champ") - (version "2.28.0") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChAMP" version)) (sha256 (base32 - "10ss0a3miqrx92vy1r1h5rv3mnjn4iyl32q86s0x59d3fvqp2cx1")))) + "1px2pm90lxwh0yn7h1kmmf94flhjs5p4i0iav7ya1xfybyg4w2zc")))) (properties `((upstream-name . "ChAMP"))) (build-system r-build-system) (propagated-inputs @@ -6022,18 +6096,19 @@ regions and to highlight copy number alterations.") (define-public r-chipseeker (package (name "r-chipseeker") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPseeker" version)) (sha256 (base32 - "0jr9mc79di0r3xrc7m27vwk85qa4fpcwp4nb77pr9s6jbv23773r")))) + "0nngygci1g8bb3rsica348zi59hskr6hf8319csia6cman89gvqm")))) (build-system r-build-system) (native-inputs (list r-knitr)) (propagated-inputs (list r-annotationdbi + r-aplot r-biocgenerics r-boot r-enrichplot @@ -6042,17 +6117,17 @@ regions and to highlight copy number alterations.") r-genomicranges r-genomicfeatures r-ggplot2 - r-ggvenndiagram r-gplots r-gtools r-dplyr r-plotrix r-dplyr r-magrittr - r-rcolorbrewer r-rtracklayer r-s4vectors - r-txdb-hsapiens-ucsc-hg19-knowngene)) + r-tibble + r-txdb-hsapiens-ucsc-hg19-knowngene + r-yulab-utils)) (home-page "https://www.bioconductor.org/packages/ChIPseeker/") (synopsis "ChIPseeker for ChIP peak annotation, comparison, and visualization") (description "This package implements functions to retrieve the nearest @@ -6069,14 +6144,14 @@ annotation, distance to TSS, and overlap of peaks or genes.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1gmspbf5bmlqgbq280lnh4m9bmhzv6d0aj15dmggizsgb9d34vp5")))) + "0q83c4dm9qbdxlh4cbdzp357fn4sa16d7dqb4s65650pcnjg3a48")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -6085,6 +6160,7 @@ annotation, distance to TSS, and overlap of peaks or genes.") r-lattice r-s4vectors r-shortread)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/chipseq") (synopsis "Package for analyzing ChIPseq data") (description @@ -6095,14 +6171,14 @@ experiments.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1mf0h2j31m57jd3s1sj8ijn9wdgbg452d79drdkxypxqvpm7b927")))) + "08jpbw7qns736zq1fwk9lyr4qm7rgzzw3hksv59zwb1458a79pzy")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -6257,21 +6333,20 @@ distribution.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.38.3") + (version "1.40.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0kryg9jb6zl4zj1wx09rmljqlhr5vdbcmdnri4q91jpggsaj9nxm")))) + "1910nvcm1lj5mcg8jdvfql6a6h1wnrgfl616gz942g4ngl18ya3p")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-biocparallel - r-geneplotter r-genomicranges r-ggplot2 r-iranges @@ -6282,7 +6357,7 @@ distribution.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list r-knitr r-rmarkdown)) (home-page "https://bioconductor.org/packages/DESeq2") (synopsis "Differential gene expression analysis") (description @@ -6295,14 +6370,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "01728hag1c5fh4n0v57k1p9ss5rqgckab4cnj5flp750myi1fbps")))) + "0z4i3lsaziq3hprk64akx7jl6b757kmd8k6gv5pn36pavc6x1a0g")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6340,13 +6415,13 @@ exploration of the results.") (define-public r-diffcyt (package (name "r-diffcyt") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "diffcyt" version)) (sha256 - (base32 "10xhvksnnn4m1hly16fwmbr28xgym6a9zkqj8y476jph4wpnhc2s")))) + (base32 "1vsn9z06vmfw6741x7dri3d9wh4rqhzak9r506y3c3h2gjjwilv1")))) (properties `((upstream-name . "diffcyt"))) (build-system r-build-system) (propagated-inputs @@ -6378,14 +6453,14 @@ adapted from transcriptomics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "009nnl3zwcsg6mh7wl3j856dpi7awkyxdy660rqmiskn7m2ah4l1")))) + "1vslg6hp498ar4l1b8rdxscz5wj1xci866j8975wr378lnymb942")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -6405,13 +6480,13 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-dittoseq (package (name "r-dittoseq") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dittoSeq" version)) (sha256 (base32 - "0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b")))) + "0g5xxzd2xvh0m1fmyzzriwnrq1ckcmb95h9yl60h5w3c3ph22438")))) (properties `((upstream-name . "dittoSeq"))) (build-system r-build-system) (propagated-inputs @@ -6449,14 +6524,14 @@ code{dittoColors()}.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0hx4als33lvdchz5s6cv2axvjyp0k8p3v0lm51jayhjcjpmihqzp")))) + "0gf4k02b5qywrg5rpg6hs9gyzcdlpw36ndgz3ca19plicair4mih")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -6489,13 +6564,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.40.2") + (version "3.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0ds34b135qd63dh3cxkp8b28270m50bn1njwr49b8svgcgzz9x09")))) + "1vss3n2m12vf6wcspfly394b8g3mfbwkkw8ihz8nqpc2iqs399rj")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -6514,13 +6589,13 @@ CAGE.") (define-public r-enmix (package (name "r-enmix") - (version "1.34.02") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ENmix" version)) (sha256 (base32 - "0rn541xfsxfdyzy3dn727bwrfpkgp12282lax7xg1j8584mk4pcf")))) + "1cwj45rnb6ra1bnd0plkjfvfsix25xr51yh6rwrfj524c35r70w1")))) (properties `((upstream-name . "ENmix"))) (build-system r-build-system) (propagated-inputs @@ -6556,14 +6631,14 @@ visualization of Illumina DNA methylation array data.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1v1in3imqbwak3v9w99l6hq8kihai5xvpgxvg7imna7jn1w8kmji")))) + "0rl5ix755055i95y5xfb4zv5gih2gkqwqia1r1b3yx12z5ybvkc6")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -6601,14 +6676,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "1m1x7xmbxwa15vzd45h16pnib944f20pwinx1pyhba5hcngkikfi")))) + "0gygyf1xq1z6vzand43n965p366zh0k3rv58gnyqa81whj4dvcq3")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics r-genomicranges r-iranges @@ -6628,14 +6703,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.48.0") + (version "2.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "08qvg1cmrln7w5z33r81kz1zjs8fcj3qbxm1crbsazvb6gdpqyyi")))) + "16wx2w70i12420022xz2zx8pizzyxb7z1pcmqn515cs89f1qcnli")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-go-db r-graph r-keggrest)) @@ -6656,19 +6731,19 @@ analysis using other methods.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.80.3") + (version "1.82.1") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "047p84qxfqqm0d0ik7fxcs37fmg0yazsn9rz7h4g24cksb45p689")))) + "1wpg8banz6s6smycfqf9hqryp4kf2gs069s7npyvpq53wy0kxyny")))) (build-system r-build-system) (native-inputs (list gfortran r-knitr)) (propagated-inputs - (list r-annotate r-annotationdbi r-biobase r-biocgenerics + (list r-annotate r-annotationdbi r-biobase r-matrixgenerics r-survival)) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") @@ -6680,13 +6755,13 @@ high-throughput sequencing experiments.") (define-public r-geneoverlap (package (name "r-geneoverlap") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GeneOverlap" version)) (sha256 (base32 - "0ii3ymysqkhyvj204zigpgjny0cglggqmvw311gvgkdi16dib1qs")))) + "1bimsayaf68j15im591r6rbvydhbmiqcp1pphd5zzg6hzp6va927")))) (build-system r-build-system) (propagated-inputs (list r-rcolorbrewer r-gplots)) @@ -6699,13 +6774,13 @@ and visualize the results.") (define-public r-genomation (package (name "r-genomation") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "098ldnh45f48145jfsbdw5dqv5yiqkfci1fy6h6gjz7nh3dvnil5")))) + "0y6a2qxxp5mnkllcq46j00069z22ixnrbkd15s007a35lhkibz21")))) (build-system r-build-system) (propagated-inputs (list r-biostrings @@ -6746,13 +6821,13 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.34.9") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0mn9ddm2xwc2b7zg0n9a056jcr61jv6v8jacxm3q8qmz6r30kfrb")))) + "072dawysgcfyhnwva38y5vf95y3b9dhpad66mwma07hrh27a6wqh")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -6773,13 +6848,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1c784ic85v64gflwwk22dh3f0m60q3z6y23d9jy3w8ydhda6gw0s")))) + "1irzcz9s97gqbyj9j71wxv2ikdfd8g14296fg33w2ykfdm80nzf0")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -6806,13 +6881,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.50.4") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1qsr433nh225pk5ngsrjrf2rfv7ynq4c8qsjfjr7khy2z9czlg6n")))) + "0sccj6py15g5ihdrpzwn7j71wkqwljay8p2yn2wkd8142cfsr7x3")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -6850,14 +6925,14 @@ extracting the desired features in a convenient format.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0k64m9f5y88p90wd87hy0ixj5ly5yi413al9p2bn10b1fjx2c451")))) + "0nxz8lvpmyllgs1ksgbha8qqs4fhppkg5casppnas9x47dj4bxph")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -6873,6 +6948,7 @@ extracting the desired features in a convenient format.") r-s4vectors r-summarizedexperiment r-variantannotation)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GenomicFiles") (synopsis "Distributed computing by file or by range") (description @@ -6884,13 +6960,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.50.2") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "13b6bm6nrxx1vgzrzpf59c2lq5w8kjq9hsch5h037f0p9w3w5z9p")))) + "0vbr8nqn4pk0w3wx94q4f44psy6lxgx4b7p8hp0vf46flwggj2lj")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -6911,13 +6987,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-glad (package (name "r-glad") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GLAD" version)) (sha256 (base32 - "0gb52ic5r6nkgm2ynm174vcvbmkbhhjgv71lsmxpxzcsb6rr7qj6")))) + "0fi7wwn0ai4bwy8wgwl4dh3fbl6zhrkcy662dc1fcnk5i7rnv3y5")))) (properties `((upstream-name . "GLAD"))) (build-system r-build-system) (inputs (list gsl)) @@ -6935,13 +7011,13 @@ regions identified.") (define-public r-globaltest (package (name "r-globaltest") - (version "5.52.1") + (version "5.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "globaltest" version)) (sha256 (base32 - "1g5dv3bw0fj8sq0hsr8c7nh6n1rzvx1bisqlyqjqq3f8lsyb51kb")))) + "0jjhhg4vi44xqlvmcd80m30m93qyd4c79i7m9jn5hz3mw211xaig")))) (properties `((upstream-name . "globaltest"))) (build-system r-build-system) (propagated-inputs @@ -6959,14 +7035,14 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") (define-public r-gostats (package (name "r-gostats") - (version "2.64.0") + (version "2.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "07chyfkq8nwxjgnlrrwza8jw996dq0ki4bzdfalj9yl1iac1pnys")))) + "1jjcjc1zp42l3gw36rr84al07ghih0cjx4p8gn8rlmv1jsz6kp1h")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -6979,6 +7055,7 @@ facilitate the use of this test for gene set testing of GO and KEGG terms.") r-graph r-rgraphviz r-rbgl)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/GOstats") (synopsis "Tools for manipulating GO and microarrays") (description @@ -6990,14 +7067,14 @@ testing and other simple calculations.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0i8fliln3v9sw9x34pqafdx1z6jkys8b11fkz4ihmw8lc8lfd0x5")))) + "0xfcgvsglcwkwsb1azmp4n4hx95fxnjk7rlwggb1f5rjw440qjnh")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -7019,13 +7096,13 @@ Enrichment Analysis} (GSEA).") (define-public r-harshlight (package (name "r-harshlight") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Harshlight" version)) (sha256 (base32 - "0asjgcnwawg8x7ql0srhb2011rvb4kr2cpsa1cy28nfmjfvdf0qm")))) + "1rg3gx42a68jqbdmbqx7lh97y0rird1lci7146hnxa4svj827d5p")))) (properties `((upstream-name . "Harshlight"))) (build-system r-build-system) (propagated-inputs @@ -7046,15 +7123,30 @@ matrix to solve the memory problem.") (define-public r-hpar (package (name "r-hpar") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hpar" version)) (sha256 (base32 - "1dls59d2ysk8ngk5c6nx7xqgc2iygbdlzf88gccf2wm8zhy8m3f4")))) + "1sg0mjada72a13xh3k6xsiaff7xj4mp76r6i8iab8nfkvng07p4i")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + (lambda _ + (setenv "HOME" "/tmp"))) + (add-after 'unpack 'avoid-internet-access + (lambda _ + (setenv "GUIX_BUILD" "yes") + (substitute* "R/zzz.R" + (("ExperimentHub::createHubAccessors.*" m) + (string-append + "if (Sys.getenv(\"GUIX_BUILD\") == \"\") {" m "}")))))))) + (propagated-inputs (list r-experimenthub)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/hpar/") @@ -7066,14 +7158,14 @@ the Human Protein Atlas project.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1ri76wwv44hgxji2bmlqi6v8gbvhr72q0d6nlgpfgfwb9sgvz62h")))) + "1p8imns26knh21r254n7i9xvy8xzz3zizx0kq4si7cdaf2b4xayi")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, @@ -7095,13 +7187,13 @@ of other R packages who wish to make use of HTSlib.") (define-public r-impute (package (name "r-impute") - (version "1.72.3") + (version "1.74.1") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "1qq80za9bkg0wqnlckvahnjz08xacwvpnflwnrmwr2xg0ifkis38")))) + "0nz8ggzk2g5w20yyhp6av6hy69kbmg3ncfpq9ppmq6p5a0msx92l")))) (native-inputs (list gfortran)) (build-system r-build-system) @@ -7115,14 +7207,14 @@ microarray data, using nearest neighbor averaging.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1j2cz929q9hwkchnzcs3mnbmhg68mm06r9bgylnbll4j5ibqicrz")))) + "1p3lwk8g14srkhl3x3i0v2d9071251ldy9964mii11k1bp2g08am")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -7140,14 +7232,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0623p6px259v000pp14c2rknjgivx9c90b626q9bln0qw6wy97zc")))) + "1zmsk5w8i3cq0983nx1d24a6awrbq7aj2wrapsnizq9gvrsrhbbb")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -7185,13 +7277,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.54.2") + (version "3.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1qch34znld9i8sy1xwpy23z2zs07nj39wkfmgfi7qw141vn6gr8b")))) + "01q0rq2xwjsqj4phym4885iblpvfwvi5nphmnq8l3ybs0ixm2g9w")))) (build-system r-build-system) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7204,32 +7296,15 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-maaslin2 (package (name "r-maaslin2") - (version "1.12.0") + (version "1.13.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Maaslin2" version)) (sha256 - (base32 "0ncvsywn9f8766gjb8nxzg82p3w30g8pjs85sy8s0bz9ilanpy89")))) + (base32 "05xha6y6ssf80l4xb7skbjafpqww2d85l4b6wn72r5djidyxxw6y")))) (properties `((upstream-name . "Maaslin2"))) (build-system r-build-system) - (arguments - (list - #:phases - #~(modify-phases %standard-phases - (add-after 'check 'remove-timestamps - (lambda _ - (with-directory-excursion - (string-append #$output "/site-library/Maaslin2/doc/demo_output/") - ;; Delete this log file with timestamps. - (delete-file "maaslin2.log") - ;; Replace PDF timestamps with an arbitrary fixed timestamp. - (with-fluids ((%default-port-encoding "ISO-8859-1")) - (substitute* (find-files "." "\\.pdf$") - (("/CreationDate \\(D:.*\\)") - "/CreationDate (D:20230301143558)") - (("/ModDate \\(D:.*\\)") - "/ModDate (D:20230301143558)"))))))))) (propagated-inputs (list r-biglm r-car @@ -7246,14 +7321,12 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") r-logging r-lpsymphony r-mass - r-mumin r-metagenomeseq r-optparse r-pbapply r-pcapp r-pheatmap r-pscl - r-rmarkdown r-robustbase r-vegan)) (native-inputs (list r-knitr)) @@ -7271,13 +7344,13 @@ of data exploration, normalization, and transformation methods.") (define-public r-made4 (package (name "r-made4") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "made4" version)) (sha256 (base32 - "0ylcigzbahic99afqk1q29d4wczmsqmp2hasvihcykybb440a6f2")))) + "1233l5160msxp85vm2h0j3k073vv5d9wj55709x4s657fi9la6ij")))) (properties `((upstream-name . "made4"))) (build-system r-build-system) (propagated-inputs @@ -7300,13 +7373,13 @@ datasets (coinertia analysis).") (define-public r-makecdfenv (package (name "r-makecdfenv") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "makecdfenv" version)) (sha256 (base32 - "0bvj5dg6yfjnhga1z8788zmb98d8shyz8pzz0ggnml87c1p2gy25")))) + "1a6kngwmc7nvzlgpnhdv4j180847gjh4i3dshld0pcvy3b6bjv8r")))) (properties `((upstream-name . "makecdfenv"))) (build-system r-build-system) (inputs (list zlib)) @@ -7327,13 +7400,13 @@ package that automatically loads that environment.") (define-public r-manor (package (name "r-manor") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MANOR" version)) (sha256 - (base32 "16b30bmyzml97cjdbh6h9ky5c4h5ws2a3g2xkxnd55sd3jg64jgx")))) + (base32 "0ili9xy7vvw17mz44lxadv1vkf3ahpks2l34qa9yfccpalwhzriw")))) (properties `((upstream-name . "MANOR"))) (build-system r-build-system) (propagated-inputs (list r-glad)) @@ -7350,13 +7423,13 @@ experiments.") (define-public r-maser (package (name "r-maser") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maser" version)) (sha256 (base32 - "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv")))) + "1ma5d1i56gw8hm2pgvzzvmdd1cm2xb42rgf5lb6sf4v47yzlyb9f")))) (properties `((upstream-name . "maser"))) (build-system r-build-system) (propagated-inputs @@ -7382,13 +7455,13 @@ and visualizaton of alternative splicing events generated by rMATS.") (define-public r-metagenomeseq (package (name "r-metagenomeseq") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metagenomeSeq" version)) (sha256 - (base32 "01wjw4kcm8ysa5sn3cqg4a9i5pyksnwmbdqp5fr6n2l9hllkc9jy")))) + (base32 "0293c531l0sjz8qxy7nrajfl081v9df0af9242017msbvyszq6wk")))) (properties `((upstream-name . "metagenomeSeq"))) (build-system r-build-system) (propagated-inputs @@ -7416,13 +7489,13 @@ correlations.") (define-public r-metaneighbor (package (name "r-metaneighbor") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MetaNeighbor" version)) (sha256 (base32 - "1gjjp5qlmv26sd3fvrd8cgv3invckxr8ldjpizpqm4mxjzifxwpm")))) + "151ip70la12kj80c0airi1yyjbj69gnkshd6kfk88wsvq7s179id")))) (properties `((upstream-name . "MetaNeighbor"))) (build-system r-build-system) (propagated-inputs @@ -7452,13 +7525,13 @@ profiles than cells of different types.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0w6wv8x1jggbvymb07b2z47myf239mwpwbgz5p5yi60qb0k7p2q9")))) + "1qi4gwlxsxr4cgs8s12qybrs89vr79xwd7n9in1af3hyn0swikn1")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -7499,13 +7572,13 @@ TAB-Seq.") (define-public r-mmuphin (package (name "r-mmuphin") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MMUPHin" version)) (sha256 - (base32 "0vpap3avmrjy187s3dva6f008al6d935kpdf816xzl5gxl7zvf62")) + (base32 "14cn1mg9ffhzy1vgschl2h0wzah3c1g67q367f2m050a3z2i2ndy")) ;; Delete generated files. (snippet '(for-each delete-file @@ -7542,7 +7615,6 @@ TAB-Seq.") ;; not seem to reference the library directly. (propagated-inputs (list r-cowplot - r-biocstyle r-dplyr r-fpc r-ggplot2 @@ -7595,14 +7667,14 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-muscat (package (name "r-muscat") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "muscat" version)) (sha256 (base32 - "061dgs3ygvr4vrc6mrmikqn4a7a5qajn7k8crbskdkg4svg8qv1a")))) + "1jcy07m8ywpgsmwkq6s7zj32w7gvxqj52j562irv2h2q429awdxk")))) (properties `((upstream-name . "muscat"))) (build-system r-build-system) (propagated-inputs @@ -7645,14 +7717,14 @@ platform that mimics both single and multi-sample scRNA-seq data.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "3.8.1") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0d0fsc4x8psfd93asi2d5kq1888s963d3s8kcihd5knqah000mh8")))) + "1p9n5afnr4cx690w9d5q1hkwqffsbnsn72wibqcl5rbqgfsvhf8h")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -7691,13 +7763,13 @@ in SNV base substitution data.") (define-public r-msa (package (name "r-msa") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msa" version)) (sha256 (base32 - "064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4")))) + "08fg4y8rmkvilsx2hxqwxa90p2wqrl4iyndp7wfjicvplmaxp708")))) (properties `((upstream-name . "msa"))) (build-system r-build-system) (propagated-inputs @@ -7722,14 +7794,14 @@ package TeXshade.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.24.2") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7")))) + "0qpgpvzg0vw45ia3dpkpfs56dj06crjrrg4i9l46bj8f2pgzcf0g")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -7767,14 +7839,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9")))) + "1mxlr76xrgp3limhr20naanhqr6b0d2wbk9l63j0pi2yckszxjjc")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (arguments @@ -7824,14 +7896,14 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-mzid (package (name "r-mzid") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0h5w5ykbziaif6m61pa5x92f2rblfgldvj9vajfhkmxj1b2ks9za")))) + "0grl7798vnpxb6nw98zj0lbvsrhkjfsyn0y15bi4v7vhyhkk26xm")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -7855,14 +7927,14 @@ specific parser.") (define-public r-mzr (package (name "r-mzr") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0p7mkvvaf25si95lpwpr65jm3dzxmgs9i0wilyb2mbxkdcz9vm71")) + "0dz9wqaawhkvswv4035xknlicia0m79r8n666s1yf59cfpmdqgs3")) (modules '((guix build utils))) (snippet '(delete-file-recursively "src/boost")))) @@ -7973,14 +8045,14 @@ Gao et al in Nature Biotechnology 2022}.") (define-public r-organism-dplyr (package (name "r-organism-dplyr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Organism.dplyr" version)) (sha256 (base32 - "1hawn8pp63kal5ml0sm3h1j1wnkq02z64sliyaf6apv7vl60ja9g")))) + "0yrd7a7c0n6c987gyy76jidpvsdwrv2097f9wkvh4y5dd1w0mk7p")))) (properties `((upstream-name . "Organism.dplyr"))) (build-system r-build-system) (propagated-inputs @@ -8012,14 +8084,14 @@ functionality of the @code{TxDb} packages (e.g., (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "11l1xqwbqs129vxd6lxdaizpp6j08spyh6799rv5wqmlymap1ykw")))) + "1pw3qd6n0xf7vq3x73612bndcqhwrqkpi29f6crazdzjcy3fivlb")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -8034,6 +8106,7 @@ functionality of the @code{TxDb} packages (e.g., r-iranges r-rbgl r-s4vectors)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/OrganismDbi") (synopsis "Software to enable the smooth interfacing of database packages") (description "The package enables a simple unified interface to several @@ -8044,13 +8117,13 @@ the fact that each of these packages implements a select methods.") (define-public r-oscope (package (name "r-oscope") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Oscope" version)) (sha256 (base32 - "0454f9yc0jmg3mcq9264wb5v2n8n0kaf801hlvsiy1xa3baj3h29")))) + "055j7y1icikqivc795hzl1l5v5ga2bfcqk2x0kivawbrqvj4yq5v")))) (properties `((upstream-name . "Oscope"))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-cluster r-ebseq r-testthat)) @@ -8070,14 +8143,14 @@ insertion module to recover the base cycle order for each oscillator group.") (define-public r-pcaexplorer (package (name "r-pcaexplorer") - (version "2.24.0") + (version "2.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaExplorer" version)) (sha256 (base32 - "0gs4az4h5mwnr3s8fq7im5p3mm4mhc0x5amjr2badqkw1fih3jp7")))) + "04r4qsiasbfb0pwqyqmw2w3qdkhgwixwffp1s8hjflwnb63hxzjx")))) (properties `((upstream-name . "pcaExplorer"))) (build-system r-build-system) (propagated-inputs @@ -8125,14 +8198,14 @@ application encapsulates the whole analysis.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.90.0") + (version "1.92.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "1cjmkfpbbfzkx6bi3r9jjx54iwkm4gl8hqa1776hxicq2x2c83s4")))) + "14awrgq56s948x74j4iv9k1yy5b7axw1kqzg827y5znjc1i3aqy6")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -8194,14 +8267,14 @@ chromosome. Both tumor-normal paired and tumor-only analyses are supported.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li")))) + "0fgsb47qrvrl4y3yr094mas22rai5h5yl9mciadd6zcpamp2p01i")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -8214,18 +8287,19 @@ proteomics packages.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0dccxsynfnhjzjk22hr5kg068zbg33g6kyhlhlhqh78582181j9m")))) + "0y6ghiwraw3whs57i31qnvlvqlbl9143wxv2yg48rp7qxipxvn6s")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs (list r-bh r-graph)) + (native-inputs (list r-knitr)) (home-page "https://www.bioconductor.org/packages/RBGL") (synopsis "Interface to the Boost graph library") (description @@ -8236,13 +8310,13 @@ the graph algorithms contained in the Boost library.") (define-public r-rcas (package (name "r-rcas") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "0wja7m3b3zr0m8nwcq5m5appsr09jdwkvvvxzh2r5mhksn0abs6p")))) + "073fhbh0pzyca90q2irbaiwj21sci8jf9ksflx9pm9fr1giy37i4")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -8286,14 +8360,14 @@ library implementing most of the pipeline's features.") (define-public r-regioner (package (name "r-regioner") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "regioneR" version)) (sha256 (base32 - "01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049")))) + "0grlqga9d6mch9l487fdll65wi0m2kpq2097igfhx185i8jvwsz1")))) (properties `((upstream-name . "regioneR"))) (build-system r-build-system) (propagated-inputs @@ -8317,17 +8391,44 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.38.0") + (version "2.39.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "1nrgnb002qv0yzmrvg59i9b5wzxda0fdkrmdi6vr15g0g7j3yry0")))) + "15h7vqdxfv7y0f82ff7a8brqnscs324x22izlkgjk2wqahnmr2l1")) + (snippet + '(for-each delete-file + (list "inst/doc/jslib/jquery-1.8.0.min.js" + "inst/extdata/jslib/jquery-1.8.0.min.js"))))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "_") + "inst/doc/jslib/jquery-1.8.0.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))) + (copy-file "inst/doc/jslib/jquery-1.8.0.min.js" + "inst/extdata/jslib/jquery-1.8.0.min.js")))))) (propagated-inputs (list r-annotate r-annotationdbi @@ -8349,7 +8450,13 @@ region sets and other genomic features.") r-r-utils r-xml)) (native-inputs - (list r-knitr)) + (list esbuild r-knitr + (origin + (method url-fetch) + (uri "https://code.jquery.com/jquery-1.8.0.js") + (sha256 + (base32 + "02vnwfxrrfsqm6qbmxyv9rdg32qyzs81d1snk62fy08gv7r62hfk"))))) (home-page "https://bioconductor.org/packages/ReportingTools/") (synopsis "Tools for making reports in various formats") (description @@ -8367,13 +8474,13 @@ browser.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.42.1") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "04qg758b98ggn8gnwppz4f441qx62jzwyscccnh2dr323x62bxhh")))) + "1akbr55lylwp20b2j351h1gcj1sc5y2j2pjjdpz43m6b7mji23a0")))) (build-system r-build-system) (propagated-inputs (list r-rhdf5filters r-rhdf5lib)) @@ -8394,22 +8501,42 @@ the available RAM.") (define-public r-rhdf5filters (package (name "r-rhdf5filters") - (version "1.10.1") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5filters" version)) (sha256 (base32 - "14rkr0fisy7qrvjikpnwxwag79205hdxy6nkpwz501li4fr1rbnp")))) + "1v9wxa5q0iwphrmkf9x70jpbq9r9rqz2hm94smqnnpfxszila49m")))) (properties `((upstream-name . "rhdf5filters"))) (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-system-libraries + (lambda _ + (substitute* "src/blosc/Makefile.in" + (("libblosc.a: blosc") "libwhatever.a:") + (("libblosc.a") + (string-append #$(this-package-input "c-blosc") + "/lib/libblosc.so")) + (("../zstd/libzstd.a") "-lzstd")) + (substitute* "src/bzip2/Makefile" + (("libH5Zbz2.so: bzip2-1.0.8/libbz2.a") "libH5Zbz2.so:") + (("./bzip2-1.0.8/libbz2.a") "-lbz2")) + (substitute* "src/zstd/Makefile" + (("libH5Zzstd.so: libzstd.a") "libH5Zzstd.so:") + (("libzstd.a") "-lzstd")) + (substitute* "src/vbz/Makefile" + (("../zstd/libzstd.a") "-lzstd"))))))) (propagated-inputs (list r-rhdf5lib)) (inputs - (list zlib)) + (list bzip2 c-blosc zlib (list zstd "lib"))) (native-inputs - (list r-knitr)) + (list r-biocstyle r-knitr r-rmarkdown)) (home-page "https://github.com/grimbough/rhdf5filters") (synopsis "HDF5 compression filters") (description @@ -8420,13 +8547,13 @@ HDF5 datasets.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0wd4hsn19msz0fkwfq7gvi97vlfpsbzzw3rjj4b6z7s5a83zir2z")))) + "18kh6vmyjmv7zklqr5ifpfixjwldxgwj550c69mqfkk7m0zk52cl")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -8450,6 +8577,7 @@ HDF5 datasets.") r-rhtslib r-s4vectors r-xvector)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") (synopsis "Interface to samtools, bcftools, and tabix") (description @@ -8485,13 +8613,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk")))) + "0gy8df0ndq6nyly4b5h3kby8k77rc4j9n7zhnliryvirpr6alm9m")))) (build-system r-build-system) (arguments `(#:phases @@ -8564,13 +8692,13 @@ differential expression analysis, RNAseq data and related problems.") (define-public r-scannotatr (package (name "r-scannotatr") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scAnnotatR" version)) (sha256 - (base32 "0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93")))) + (base32 "0mxq2dknrhgj1487kfshkayx963c7qdgxwmlh9fbfr0lwc7gljfn")))) (properties `((upstream-name . "scAnnotatR"))) (build-system r-build-system) (propagated-inputs @@ -8601,13 +8729,13 @@ cell types based on specific research needs.") (define-public r-scdblfinder (package (name "r-scdblfinder") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDblFinder" version)) (sha256 - (base32 "0gslh28rycx0p6a6fmzbsqy1hg2sn3pp5blxgw01qk9f0ank7szi")))) + (base32 "0lvacrgfj9i8mwlcv5ykxs69hd3bm6bvr6fsddxffsr7cckpn31w")))) (properties `((upstream-name . "scDblFinder"))) (build-system r-build-system) (propagated-inputs @@ -8683,13 +8811,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.20.2") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "00zqvjfn1pqza5gl3jfr10fvcrq6gpw9hfjcxjsm4f5p7ldnhpw0")))) + (base32 "184dp319967ba9wx2g1v4rivwy3csr44s7in1jk91d5hwj28nk09")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -8725,20 +8853,19 @@ different experiment.") (define-public r-scry (package (name "r-scry") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scry" version)) (sha256 (base32 - "0vx6fi8hnxms6d3hm3qxkrdx1qpyd7vhwdk7ds98ads070miqr21")))) + "0406slld468m9lxswv1akcdmap6izvzz6zljyrs5av546nfxpmrz")))) (properties `((upstream-name . "scry"))) (build-system r-build-system) (propagated-inputs (list r-biocsingular r-delayedarray r-glmpca - r-hdf5array r-matrix r-singlecellexperiment r-summarizedexperiment)) @@ -8757,14 +8884,14 @@ single-cell RNA-seq.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1xlxi1iaqj7iabzbx15j6pk4551dyj6pa6a6qf5ffr3v7k2pmznp")))) + "0727yrmm194gskrcpmq4fh0qmi6dnp70gx627psrpvzlk6vlcl8k")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (native-inputs @@ -8780,13 +8907,13 @@ Stephens (1990).") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "17nvxy8kdc1k0kyf0qny6jp3gzr024q37mmh5x18jjr794hnf9s5")))) + "033hss67dxi6fbvn6ya7vc61f60m20hwms9kmdia0icyp8nv2yil")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -8803,19 +8930,20 @@ reference point and sorted by a user defined feature.") (define-public r-shinymethyl (package (name "r-shinymethyl") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "shinyMethyl" version)) (sha256 (base32 - "1xbadc4xszcqh211r8z0wp417f17aczz834icli17mcsl996ln3a")))) + "1rqwwglj0475gr14bxazfmcvsy7rq6nlw2zcswa684751wy15w0r")))) (properties `((upstream-name . "shinyMethyl"))) (build-system r-build-system) (propagated-inputs - (list r-biocgenerics - r-illuminahumanmethylation450kmanifest - r-matrixstats + (list r-biobase + r-biocgenerics + r-htmltools + r-matrixgenerics r-minfi r-rcolorbrewer r-shiny)) @@ -8830,14 +8958,14 @@ methylation array data. Both the 450k and EPIC array are supported.") (define-public r-shortread (package (name "r-shortread") - (version "1.56.1") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1dvnjjc6cwn9wicki3ff3w3zx7i0szj0lnfw4n6lbmipg4ia5bkb")))) + "0wpr3ksr7j5yk6m1zaa47dwdgznajsz8as4p9vf7schaqvhq1wc4")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -8873,14 +9001,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "130x5hy6jzglc6clwanh2kmhw567i802w620ffs3977kjfpjsjgy")))) + "1vs57j361fbwv7vaybs71vc208qn76djmbmakhwwcvxwrx77jp5f")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -8914,13 +9042,13 @@ and comparing the clusterings.") (define-public r-transcriptr (package (name "r-transcriptr") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "transcriptR" version)) (sha256 - (base32 "03v8xn777vyma82ma5dzk07i1g7406cvsybdz4bf6hj8bgx5ynw7")))) + (base32 "0i38zs33drzk9szy2mdfs9ff9c3ccjgiyyynrrsinrx0szc8l22r")))) (properties `((upstream-name . "transcriptR"))) (build-system r-build-system) (propagated-inputs @@ -8964,14 +9092,14 @@ able to deal also with novel and case specific events.") (define-public r-trajectoryutils (package (name "r-trajectoryutils") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TrajectoryUtils" version)) (sha256 (base32 - "130w4vpsmrkg458n3wbhvlchg171gjqybvs2w14bxa608f3fzw03")))) + "1q3c226fskl45gq28xj2w5paz2s9n9kxm0bkkgg0329w399cs09k")))) (properties `((upstream-name . "TrajectoryUtils"))) (build-system r-build-system) @@ -8991,13 +9119,13 @@ structures to hold pseudotime inference results.") (define-public r-scds (package (name "r-scds") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scds" version)) (sha256 (base32 - "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd")))) + "059gahl679if8xsfgpxmi3h9fiagb6v08rd6rs7yv96s3pb8qywn")))) (properties `((upstream-name . "scds"))) (build-system r-build-system) (propagated-inputs (list r-dplyr @@ -9019,13 +9147,13 @@ scRNA-seq data computationally.") (define-public r-slingshot (package (name "r-slingshot") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "slingshot" version)) (sha256 (base32 - "00h9iid2z9r55l4hlaa1q0nkbcfq0f7k2afkw4ymjwhm1b8yqj33")))) + "1xr17rg8nfpcvdwa19qrcaqffkz048l5lkqlm6gw0abm8bg2k8x7")))) (build-system r-build-system) (propagated-inputs (list r-igraph @@ -9091,13 +9219,13 @@ tools either included in speaq or available elsewhere on CRAN.") (define-public r-stager (package (name "r-stager") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "stageR" version)) (sha256 - (base32 "1layvv9akzijw2br9jzw6cwxn2rimha4m48fm8wn465n1nqcns0m")))) + (base32 "0advih0g2g5w8bx9f21chz8a66f4v84qn3p5skxi084pp142v5ms")))) (properties `((upstream-name . "stageR"))) (build-system r-build-system) (propagated-inputs (list r-summarizedexperiment)) @@ -9114,13 +9242,13 @@ Biology at (define-public r-stringdb (package (name "r-stringdb") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "STRINGdb" version)) (sha256 - (base32 "0qpss8fcf8ll47jv45ypsqd9jf7ajdiya7w4mw1wysk76spcwllm")))) + (base32 "0mcp9zzbayz208b573ll69glz63b2pnrxsl900y9zd9crim6vck4")))) (properties `((upstream-name . "STRINGdb"))) (build-system r-build-system) (propagated-inputs @@ -9147,13 +9275,13 @@ that integrates the various evidences.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "04vh1j2cv3qfs4q4w4xx5rn61kxrxmj5ghi54m602981cm02c3hw")))) + (base32 "0gkps2pls9bpqr8sxm8zwdkn156g8r6mhf4bx17nif5s35qld1rb")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -9184,13 +9312,13 @@ involving two separate genomic loci encoded as GRanges objects.") (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.28.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0897v6x1ki4m7kajnd60yv5qj6xa1293sj572b4dhcnfjvsf9rcn")))) + "0wj82nmqg9g8663pg5f4h7hqhr1q4ghhiif2p7x1pxmh425sn554")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -9203,6 +9331,7 @@ involving two separate genomic loci encoded as GRanges objects.") r-iranges r-matrix r-matrixgenerics + r-s4arrays r-s4vectors)) (native-inputs (list r-knitr)) @@ -9218,14 +9347,14 @@ samples.") (define-public r-sva (package (name "r-sva") - (version "3.46.0") + (version "3.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0c1b7w4rvyy8i0jygj8g9xgf46rmgx8bpdlp2x4fdjr9xsrsl23g")))) + "1f6ia57fn2sn7c2zdfswvj9kx8xayssrgf5q6hrr9nrxc0jq19g3")))) (build-system r-build-system) (propagated-inputs (list r-edger @@ -9249,14 +9378,14 @@ unmodeled, or latent sources of noise.") (define-public r-systempiper (package (name "r-systempiper") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0lwc4d4k6qmnwsh8fpp5rmiaxhzwl2f0dhzs23ska5xy04466r49")))) + "1yg650xkhmp6gcikiiv63g47k1xycg2mj8wxfnihgmlmlw4433yk")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -9292,13 +9421,13 @@ annotation infrastructure.") (define-public r-topgo (package (name "r-topgo") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1ripdn7mcabh96bm4p807dbwj7jv05a54kss4snhz84svqq383m4")))) + "0avjjvih387qhw8n4vjz4jq66q7sicgacsw53b85lq2c6ppib662")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -9325,13 +9454,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-tximport (package (name "r-tximport") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn")))) + "0km1vfn4jcp05jk5srrqanjngq6ghh5im6h1c424b926g9s7w7k1")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -9383,13 +9512,13 @@ R, enabling interactive analysis and visualization of genome-scale data.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.44.1") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "13zim7dglsd5w39v22d2qa3d1h5dx33c1r4fz3vzri64kac0lhzx")))) + "0masx496cd4ypz6r0l8kk8vi81sipqdnx4iyifjvkrds1p87mvsm")))) (properties `((upstream-name . "VariantAnnotation"))) (propagated-inputs @@ -9421,14 +9550,14 @@ coding changes and predict coding outcomes.") (define-public r-vsn (package (name "r-vsn") - (version "3.66.0") + (version "3.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1k77rg5jf646m1pn59qhlsbb9fzhlpnrj4dzxagknawcbpnnjl0z")))) + "0i6c0wyhj0gcq0mw13zyk60cza2baq4yrj1n2dzqgsqkmhm5lfla")))) (build-system r-build-system) (propagated-inputs (list r-affy r-biobase r-ggplot2 r-lattice r-limma)) @@ -9490,13 +9619,13 @@ inference.") (define-public r-xina (package (name "r-xina") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XINA" version)) (sha256 - (base32 "1c97lsb5shixh4n4mi9kh4gz4qnia9vq736rnzxbs03n5bvlmwlq")))) + (base32 "1byk8xgn9rwfbi677b99ysxi4a9n58fr3hbnwjzhnziy2n2cd703")))) (properties `((upstream-name . "XINA"))) (build-system r-build-system) (propagated-inputs @@ -9526,13 +9655,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.") (define-public r-xmapbridge (package (name "r-xmapbridge") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xmapbridge" version)) (sha256 - (base32 "0wxr3db2daj4xlr9df6iqwm00m71kln7rhqnq2ckdsricblanhs7")))) + (base32 "09pskmhjymqvhk26mk5yy1k195v536a2qp4k6xdd67xhf5ag260i")))) (properties `((upstream-name . "xmapbridge"))) (build-system r-build-system) (home-page "https://git.bioconductor.org/packages/xmapbridge") @@ -9553,13 +9682,13 @@ describing each of the graphs.") (define-public r-xvector (package (name "r-xvector") - (version "0.38.0") + (version "0.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "0ygdyh3s4qsaay930a5lbnmgh6a4gqp5ck9ww466yk0jyk1hxfp9")))) + "1v10hfz658gnb6p7pzdl28jbyypv91wx70i0dvi384nfgznhvmj2")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -9587,13 +9716,13 @@ describing each of the graphs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "0c75mf0iw6bgwrn3zxpz1dz03aw7p6a1mfhssk6i1mp24avic9lb")))) + "0x3d5kihckqnfjkc7dxk6mc194vwwr03jfjx2qh15g5494gfmm53")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -9606,13 +9735,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0b14v6lyhfapmfj8j729k5cmgxc4df6wsk2rds0q4y6z4hiwgmxy")))) + (base32 "0gn134nvgf86gnf4d4fvrvjyy3pvk3rpdabzyi4rzrpjprycf4sb")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -9638,14 +9767,14 @@ saving AnnData objects to disk.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "094v4skdvsnc7bp3acj801ih022w9k96f2b857326vd19khz0ava")))) + "03x90l7rvxk0z03p5immqbyyhiygi3mkik636al1cjdcxl9dr5f8")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -9663,14 +9792,14 @@ saving AnnData objects to disk.") (define-public r-oligoclasses (package (name "r-oligoclasses") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "oligoClasses" version)) (sha256 (base32 - "1ik9xfx6g4gf54hm5f5prip1iz6694czpbhlgwd3p9qh8ddndgp8")))) + "0i745q2kx7rdfbkz3cwzzp1m4diny25mc301vy0sh4z5lpi5mdm8")))) (properties `((upstream-name . "oligoClasses"))) (build-system r-build-system) (propagated-inputs @@ -9698,14 +9827,14 @@ packages.") (define-public r-oligo (package (name "r-oligo") - (version "1.62.2") + (version "1.64.1") (source (origin (method url-fetch) (uri (bioconductor-uri "oligo" version)) (sha256 (base32 - "19n0nvgyv2hzzcla93w2bzxvfdqg6walh0s1yykwl5b7ni4cazg9")))) + "0gs26h0hm8xlv3aayz4w0vwmw15x5602g02728spsm3n0qra3b1j")))) (properties `((upstream-name . "oligo"))) (build-system r-build-system) (inputs (list zlib)) @@ -9734,13 +9863,13 @@ Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (define-public r-quantsmooth (package (name "r-quantsmooth") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantsmooth" version)) (sha256 - (base32 "1adwws3brb01d4g6yidipnd8akkiyc3gpdr876hy57qnmcq8xipp")))) + (base32 "05lja0viz5jgc7g3b8qfhd1x596vczid0dz8278qpl4zwv9i17vx")))) (properties `((upstream-name . "quantsmooth"))) (build-system r-build-system) (propagated-inputs (list r-quantreg)) @@ -9761,14 +9890,14 @@ on the location of the probe, and other useful tools.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1dsia1c9ir989aqrgl5j5v4bysm3pyw9225yrcajiwgl8fxymph4")))) + "1552390pf3wrrir6c9xshgll69a33fhbdnh2cvpnznma1ag490ki")))) (build-system r-build-system) (propagated-inputs (list r-ggplot2 r-reshape2)) @@ -9816,13 +9945,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1hk2y7r734wdd56f18l03kyq9p35kv653a5f7z2cjkq37gvcqrd1")))) + "1k02w2jk0s65x1l2axi80fk60nxyx8jbgkax5pxwrsbv7l84n3bl")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -9832,7 +9961,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.") r-rcppeigen r-rcppnumerical r-summarizedexperiment)) - (native-inputs (list r-knitr)) + (native-inputs (list r-knitr r-rmarkdown)) (home-page "https://bioconductor.org/packages/apeglm") (synopsis "Approximate posterior estimation for GLM coefficients") (description "This package provides Bayesian shrinkage estimators for @@ -9843,13 +9972,13 @@ posterior for individual coefficients.") (define-public r-greylistchip (package (name "r-greylistchip") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GreyListChIP" version)) (sha256 (base32 - "02qzvs8fmh79g4cc5j2gxj1wazpmly7vjr527qlsgi3jmc3swxgz")))) + "1sfpf9msnzyrc8b0xzc2406bq2gkcwrrhv7fa9ynqv2ip6xwsc8s")))) (properties `((upstream-name . "GreyListChIP"))) (build-system r-build-system) (propagated-inputs @@ -9870,14 +9999,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.8.4") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "1gil19qk4wc695sl7r789xnqyv748n4jdhaighkjy5hfp9xaaax7")))) + "1p5fxfpvjz85a2n1jsmj3niqzymnlsja9b53q2yxvj327qq58z8a")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -9948,13 +10077,13 @@ processing to visualization and annotation.") (define-public r-mbkmeans (package (name "r-mbkmeans") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mbkmeans" version)) (sha256 (base32 - "1ghv2j88p3sppqph3wxpm8z84nw7bi4idkn11wf806d8h1krfjm7")))) + "0c48ycgba1m10p1w2qz9r7yxw15nqzlz8fp44d6lbrvj3svmgjwi")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -9977,17 +10106,47 @@ processing to visualization and annotation.") large datasets, including support for on-disk data representation.") (license license:expat))) +(define-public r-multibac + (package + (name "r-multibac") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MultiBaC" version)) + (sha256 + (base32 "1qwf1mvw81hb929xpnx5x910f7qnax9lkylhwzcdw1814s4zj25i")))) + (properties `((upstream-name . "MultiBaC"))) + (build-system r-build-system) + (propagated-inputs + (list r-ggplot2 + r-matrix + r-multiassayexperiment + r-pcamethods + r-plotrix + r-ropls)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/MultiBaC") + (synopsis "Multiomic batch effect correction") + (description + "MultiBaC is a strategy to correct batch effects from multiomic datasets +distributed across different labs or data acquisition events. MultiBaC is +able to remove batch effects across different omics generated within separate +batches provided that at least one common omic data type is included in all +the batches considered.") + (license license:gpl3))) + (define-public r-multtest (package (name "r-multtest") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "multtest" version)) (sha256 (base32 - "0ciz0fl0pzm4hjqw8af32s540lwjbkwvwnzgbfwadax40hgjs0g7")))) + "19c6l8pkyp0m2zdzhr81cnmx5lqf501sap9h6ig5iiv66sf2ysmz")))) (build-system r-build-system) (propagated-inputs (list r-survival r-biocgenerics r-biobase r-mass)) @@ -10015,16 +10174,17 @@ expressed genes in DNA microarray experiments.") (define-public r-graph (package (name "r-graph") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "1hdbxjvgkxb9m341i9qbskb41g2z8qifkhgkpj2xb20s2dnxn3cc")))) + "184izzxc8bpagcac8wqinjp8kmf9zpvjibl0g32nnr64kp9f4rsn")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/graph") (synopsis "Handle graph data structures in R") (description @@ -10054,6 +10214,50 @@ expressed genes in DNA microarray experiments.") fitting of some classes of graphical Markov models.") (license license:gpl2+))) +;; This is a CRAN package, but it depends on a bunch of Bioconductor packages. +(define-public r-ggpicrust2 + (package + (name "r-ggpicrust2") + (version "1.6.3") + (source (origin + (method url-fetch) + (uri (cran-uri "ggpicrust2" version)) + (sha256 + (base32 + "1rw8p1wjj3pmmccyqkl0smgnqz2s4f22hy4kyl91w8ck64xmplzs")))) + (properties `((upstream-name . "ggpicrust2"))) + (build-system r-build-system) + (propagated-inputs (list r-aldex2 + r-aplot + r-deseq2 + r-dplyr + r-edger + r-ggally + r-ggplot2 + r-ggprism + r-lefser + r-limma + r-maaslin2 + r-metagenomeseq + r-microbiomestat + r-patchwork + r-phyloseq + r-readr + r-summarizedexperiment + r-tibble + r-tidyr)) + (home-page "https://github.com/cafferychen777/ggpicrust2") + (synopsis "Make PICRUSt2 output analysis and visualization easier") + (description + "This package provides a convenient way to analyze and visualize PICRUSt2 +output with pre-defined plots and functions. It allows for generating +statistical plots about microbiome functional predictions and offers +customization options. It features a one-click option for creating +publication-level plots, saving time and effort in producing +professional-grade figures. It streamlines the PICRUSt2 analysis and +visualization process.") + (license license:expat))) + ;; This is a CRAN package, but it depends on a Bioconductor package, r-graph. (define-public r-perfmeas (package @@ -10081,13 +10285,13 @@ a given recall, F-score for single and multiple classes are available.") (define-public r-pepsnmr (package (name "r-pepsnmr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PepsNMR" version)) (sha256 (base32 - "02i29jinawssqlb33wvj0h9w6cfcvamlyfxdynd38jmwx23l15l5")))) + "17rbadvay3kbp4r6p023yww4biw9cl359q200ciygr7d2ffcas85")))) (properties `((upstream-name . "PepsNMR"))) (build-system r-build-system) (propagated-inputs @@ -10137,14 +10341,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.32.0") + (version "3.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "13syh3mvqpaqgfndcrwdmn7815f4myxhzjga9a9q3lspci25rvy6")))) + "0y9qskkdkl2vdbn66md4xisny0i7g2biasylp357vrkv41d3al6l")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -10191,13 +10395,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "05a83gh5bvgadi2msgql5nmcgr8zp398rhdbmiqna608hqbymyq9")))) + "17a4gvc1bgiym6z5dy0cigvary4knc4bpmq9bymjlwsg9337b4wg")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -10218,12 +10422,12 @@ incompatibilities.") (define-public r-marray (package (name "r-marray") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "marray" version)) (sha256 - (base32 "1bad4cjxv22h6vxxn86mxp7xvxhhzj81pikxq3h3hc2a858qfkgs")))) + (base32 "1z8fx47ng1av8nfpk0i7wpb8k8lsrn66k613p36mbh19m5fx05ks")))) (build-system r-build-system) (propagated-inputs (list r-limma)) @@ -10237,12 +10441,12 @@ normalization and quality checking.") (define-public r-cghbase (package (name "r-cghbase") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHbase" version)) (sha256 - (base32 "01n1z525h4h6yr3jfalgjg2g6lhd77sc3n33q0485x7l6xqv1dvp")))) + (base32 "1r050acahvfp2ib88sy9xj4yjzy2d8h73hndi1s075h0zv12mjj7")))) (properties `((upstream-name . "CGHbase"))) (build-system r-build-system) (propagated-inputs @@ -10256,12 +10460,12 @@ the @code{arrayCGH} packages.") (define-public r-cghcall (package (name "r-cghcall") - (version "2.60.0") + (version "2.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CGHcall" version)) (sha256 - (base32 "0860w2vf662qqii09pjdx85yl346jcldxiikhbwv0vg86blwb2g2")))) + (base32 "02d8j0al062k33h6n3ihn7kwbqp3pjwg9zzbr45ay1m1jm6bappi")))) (properties `((upstream-name . "CGHcall"))) (build-system r-build-system) (propagated-inputs @@ -10275,12 +10479,12 @@ the @code{arrayCGH} packages.") (define-public r-qdnaseq (package (name "r-qdnaseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QDNAseq" version)) (sha256 - (base32 "1qv3vmc6i7r35pqhi45hmvg8h7v3bl82lv7yifs59k250zsdls59")))) + (base32 "0lcf5zkv44s7xsa2svxia7inv6iz2k1kilfj5zcq80r339pj3vx4")))) (properties `((upstream-name . "QDNAseq"))) (build-system r-build-system) (propagated-inputs @@ -10331,14 +10535,14 @@ more complex hypotheses) via empirical Bayesian methods.") (define-public r-chipcomp (package (name "r-chipcomp") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPComp" version)) (sha256 (base32 - "1wnc7zrnnxk3nlk2l9y4il75dzirndp4vs5ivxn5rzqr6p7h4bhw")))) + "1v27bqik5cgcvs1kb67s52r56v6fakvmi81iybvvvbxvcn1dmy9r")))) (properties `((upstream-name . "ChIPComp"))) (build-system r-build-system) (propagated-inputs @@ -10365,14 +10569,14 @@ datasets.") (define-public r-riboprofiling (package (name "r-riboprofiling") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RiboProfiling" version)) (sha256 (base32 - "0wmmpcabi1ngwmvfhxkp44kj1wvzyrcckkrzpjlzcq016lr67iwn")))) + "0qgzq82v4glkc0krk81zj9z71cnrvflsf1w45r9zmaw6bq45rfqd")))) (properties `((upstream-name . "RiboProfiling"))) (build-system r-build-system) (propagated-inputs @@ -10434,14 +10638,14 @@ parsing of genetic sequencing data from ribosome profiling experiments.") (define-public r-interactionset (package (name "r-interactionset") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "InteractionSet" version)) (sha256 (base32 - "1nk8jhabbrirpyjd1wdy2fjk8y2qi1bsjmgqzh0qi1c83n0ccz5d")))) + "15bvjhwh7v4ldg5q52h1y5ks75qw85zynnybcaccypws3zlwvacn")))) (properties `((upstream-name . "InteractionSet"))) (build-system r-build-system) @@ -10468,14 +10672,14 @@ experiments.") (define-public r-genomicinteractions (package (name "r-genomicinteractions") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicInteractions" version)) (sha256 (base32 - "0l14hz5pr0wlin46y8ycpvk5hp2ld9ajx11y85rw5hlwv50byfbb")))) + "0qhb2mm5nynnw0cj5da0i6hb1bz7cyns0gp7xy0wscmfyh2wahbv")))) (properties `((upstream-name . "GenomicInteractions"))) (build-system r-build-system) @@ -10509,14 +10713,14 @@ information and producing various plots and statistics.") (define-public r-ctc (package (name "r-ctc") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ctc" version)) (sha256 (base32 - "098a65fk9la639sqihhsghhgb3hyzv35j6akph908zwq5grsv0c5")))) + "0ph22v1an2havnh9sm7hms0q2pq4fjad2cm4dffiy3344cv70sn1")))) (build-system r-build-system) (propagated-inputs (list r-amap)) (home-page "https://bioconductor.org/packages/ctc/") @@ -10529,14 +10733,14 @@ trees and clusters to other programs.") (define-public r-goseq (package (name "r-goseq") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "goseq" version)) (sha256 (base32 - "0x89lv84l3qcahca54njcza326553zij2xyagy18mwlprdrq4iy8")))) + "1r13n64s9fbx951yaa4mpna71vynbkjz78irk96yzh2x2zzxpjvx")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -10555,16 +10759,68 @@ defined categories which are over/under represented in RNA-seq data.") (define-public r-glimma (package (name "r-glimma") - (version "2.8.0") + (version "2.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Glimma" version)) (sha256 (base32 - "1fskabpd3xlrbhqvzam9ibpxmbdys7y1b265np8hz4k704ww1g22")))) + "0171wizl516chzzwnbc2z2bf5sk4a491fcs4yhq5ycqaqpjmbg35")) + (modules '((guix build utils))) + (snippet + '(with-directory-excursion "inst/htmlwidgets/lib/" + (for-each delete-file + ;; XXX: we keep inst/v1/js/glimma.min.js because + ;; it's not clear how to build it. + (cons "vega/vega.min.js" + (find-files "datatables" + "\\.min\\.js$"))))))) (properties `((upstream-name . "Glimma"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/" + (let ((files (list "datatables/Buttons-1.6.1/js/buttons.bootstrap.js" + "datatables/Buttons-1.6.1/js/buttons.bootstrap4.js" + "datatables/Buttons-1.6.1/js/buttons.colVis.js" + "datatables/Buttons-1.6.1/js/buttons.flash.js" + "datatables/Buttons-1.6.1/js/buttons.foundation.js" + "datatables/Buttons-1.6.1/js/buttons.html5.js" + "datatables/Buttons-1.6.1/js/buttons.jqueryui.js" + "datatables/Buttons-1.6.1/js/buttons.print.js" + "datatables/Buttons-1.6.1/js/buttons.semanticui.js" + "datatables/Buttons-1.6.1/js/dataTables.buttons.js" + "datatables/DataTables-1.10.20/js/dataTables.bootstrap.js" + "datatables/DataTables-1.10.20/js/dataTables.bootstrap4.js" + "datatables/DataTables-1.10.20/js/dataTables.foundation.js" + "datatables/DataTables-1.10.20/js/dataTables.jqueryui.js" + "datatables/DataTables-1.10.20/js/dataTables.semanticui.js" + "datatables/DataTables-1.10.20/js/jquery.dataTables.js" + "datatables/JSZip-2.5.0/jszip.js" + "datatables/Scroller-2.0.1/js/dataTables.scroller.js" + "datatables/Scroller-2.0.1/js/scroller.bootstrap.js" + "datatables/Scroller-2.0.1/js/scroller.bootstrap4.js" + "datatables/Scroller-2.0.1/js/scroller.foundation.js" + "datatables/Scroller-2.0.1/js/scroller.jqueryui.js" + "datatables/Scroller-2.0.1/js/scroller.semanticui.js" + "datatables/datatables.js" + "datatables/jQuery-1.12.4/jquery-1.12.4.js" + "vega/vega.js"))) + (for-each (lambda (source) + (let ((target (string-append (basename source ".js") ".min.js"))) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target)))) + files)))))))) (propagated-inputs (list r-deseq2 r-edger @@ -10574,7 +10830,7 @@ defined categories which are over/under represented in RNA-seq data.") r-s4vectors r-summarizedexperiment)) (native-inputs - (list r-knitr)) + (list esbuild r-knitr)) (home-page "https://github.com/Shians/Glimma") (synopsis "Interactive HTML graphics") (description @@ -10588,13 +10844,13 @@ information.") (define-public r-glmgampoi (package (name "r-glmgampoi") - (version "1.10.2") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "glmGamPoi" version)) (sha256 (base32 - "1ihjqzdhx6k99gdd4556xxn9822sblg6vmblcmbzml01bhv6xzar")))) + "05v9lrjbipz9av1gb0x8kd9mkivxy13wjbs5g6rdw3y72gqqv91d")))) (properties `((upstream-name . "glmGamPoi"))) (build-system r-build-system) (propagated-inputs @@ -10609,7 +10865,8 @@ information.") r-rcpparmadillo r-rlang r-singlecellexperiment - r-summarizedexperiment)) + r-summarizedexperiment + r-vctrs)) (native-inputs (list r-knitr)) (home-page "https://github.com/const-ae/glmGamPoi") (synopsis "Fit a Gamma-Poisson Generalized Linear Model") @@ -10623,14 +10880,14 @@ experiments.") (define-public r-rots (package (name "r-rots") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROTS" version)) (sha256 (base32 - "1wirblji4ckiwrvnh14cfwc9cjypazbaqr00ka5ndyz39cc31shn")))) + "0b2fl4wn696ia2kxihc6088ncnvd87ffq40bz58qi1bhq6krcmwv")))) (properties `((upstream-name . "ROTS"))) (build-system r-build-system) (propagated-inputs @@ -10646,14 +10903,14 @@ in omics data.") (define-public r-plgem (package (name "r-plgem") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "plgem" version)) (sha256 (base32 - "0hnhfdrlg4907dc4s17cy4kgmq5nr616f1wi7jn72acxwqfl4bk8")))) + "1kzrscaqsrsvdq2c9g93l7bjmv1s5p1l3cbrz6skkqls9h4gsw08")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-mass)) @@ -10670,14 +10927,14 @@ genes or proteins in these datasets.") (define-public r-inspect (package (name "r-inspect") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "126cbanan2fr916spacw6lm8hzkys56k7z3gq0r351zd7q13gky3")))) + "1nyfl78fjj956bk1xf32k3jdqhlffx6grbl7vajn48q5ldsx8kcx")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -10716,14 +10973,14 @@ modeling the rates that determines changes in mature mRNA levels.") (define-public r-dnabarcodes (package (name "r-dnabarcodes") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNABarcodes" version)) (sha256 (base32 - "18sivwzl8gk52dnhwls0i4imw78rkjlwbfrcaas1i53q0bmw15i5")))) + "1jys0lj92zkqa3bb22fg35q5y8ij5pqhy3yvzg8zc8bjpzdvrg3a")))) (properties `((upstream-name . "DNABarcodes"))) (build-system r-build-system) (propagated-inputs @@ -10743,14 +11000,14 @@ demultiplexed, i.e. assigned to their original reference barcode.") (define-public r-ruvseq (package (name "r-ruvseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RUVSeq" version)) (sha256 (base32 - "1qb4k7pm8w86d2p9q2r4n63iyi34wdib5x9rsjx4vhcxrnzyyygm")))) + "0kxaaqf6py7kfndgpd0faxv6g610zj16pyvn9b4x9s3b22ib06j1")))) (properties `((upstream-name . "RUVSeq"))) (build-system r-build-system) (propagated-inputs @@ -10768,14 +11025,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p")))) + "1i4b37n9darizfq9i4vvbnxgrwhkvvd25a4cpfjv7nqywjfbsfjd")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -10796,14 +11053,14 @@ achieved for all methods using the BiocParallel framework.") (define-public r-scaledmatrix (package (name "r-scaledmatrix") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ScaledMatrix" version)) (sha256 (base32 - "0lxr6z9zdrgvm06inc1d8gl2agqmbjvgs8f5ryn5x68hqlnchnl1")))) + "0xhw77w28r3agv0hw7fjpn1fp2p9bz7kdzwzx7gsa8411nffmd4d")))) (properties `((upstream-name . "ScaledMatrix"))) (build-system r-build-system) (propagated-inputs @@ -10822,18 +11079,19 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1xl8497ya79hlp3v3fihnz9grwni29v6860i273lrpcljv8868l9")))) + "0vix0mmx4idnxj2qaslgqrrgh97fk6p3g9p7lnf3l0915gwks1p1")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs (list r-ape + r-cli r-dplyr r-jsonlite r-magrittr @@ -10854,13 +11112,13 @@ platform for merging tree with associated data and converting file formats.") (define-public r-treesummarizedexperiment (package (name "r-treesummarizedexperiment") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TreeSummarizedExperiment" version)) (sha256 (base32 - "136zgpn1l059i64gj6iappr6nz42z4wbxlg3zpc5npwkqrz3val2")))) + "1grnz82a7l5dpwssc24yxhllqdcvza2gc4h4cc6zxjcdg5r4l1ra")))) (properties `((upstream-name . "TreeSummarizedExperiment"))) (build-system r-build-system) (propagated-inputs @@ -10887,14 +11145,14 @@ data.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.6.2") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "177nq6arhxp0x6zsf2c6cn3xxwfk65dihbpni6mb9ifgnmfqdjmx")))) + "174bdjqvq51rpdyjlcwgbxfmkpsbz6m94ymmhmsq3x39xlcbrq7y")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -10925,14 +11183,14 @@ data.") (define-public r-metapod (package (name "r-metapod") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "metapod" version)) (sha256 (base32 - "06ala1qz9bfq7nnj92m0c5r85kk7h4zrljjh0hgrap5sjlsm09bb")))) + "0lr2sgbgdbqq626nsm3vyhghs8nalg5cxycr4cwsqh9nqrmip3wa")))) (properties `((upstream-name . "metapod"))) (build-system r-build-system) (propagated-inputs @@ -10954,14 +11212,14 @@ missing values and weighting where appropriate.") (define-public r-biocsingular (package (name "r-biocsingular") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSingular" version)) (sha256 (base32 - "041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk")))) + "1a33zsw353pryq30178sbj9jzsmb4m7spqbx11hsicri8s1c0lb9")))) (properties `((upstream-name . "BiocSingular"))) (build-system r-build-system) (propagated-inputs @@ -10989,14 +11247,14 @@ possible, parallelization is achieved using the BiocParallel framework.") (define-public r-destiny (package (name "r-destiny") - (version "3.12.0") + (version "3.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "destiny" version)) (sha256 (base32 - "0rgd723azjrdxv441k96vircqb18w31q0ljhksbdrvcp9qb85r6i")))) + "0hc85dq68h7dy5jcflpjj05231ny7na9i4lksfsw89jhmxgzhacd")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11021,8 +11279,7 @@ possible, parallelization is achieved using the BiocParallel framework.") r-tidyr r-tidyselect r-vim)) - (native-inputs - (list r-knitr r-nbconvertr)) ; for vignettes + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/destiny/") (synopsis "Create and plot diffusion maps") (description "This package provides tools to create and plot diffusion @@ -11033,14 +11290,14 @@ maps.") (define-public r-savr (package (name "r-savr") - (version "1.36.0") + (version "1.37.0") (source (origin (method url-fetch) (uri (bioconductor-uri "savR" version)) (sha256 (base32 - "1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply")))) + "13wiw7isdmpwhynxjrhimy9yglcz1108k7nwa98vq9czq49zpada")))) (properties `((upstream-name . "savR"))) (build-system r-build-system) (propagated-inputs @@ -11055,14 +11312,14 @@ Viewer (SAV) files, access data, and generate QC plots.") (define-public r-chipexoqual (package (name "r-chipexoqual") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPexoQual" version)) (sha256 (base32 - "0k4vbdwpp7z06fzjgqnmrx2yllayc0z2baj26bh4vji5vb48k9ik")))) + "1iysqs2k0xxiwd48ymahf6rywwj9ingjcfmnhx9d1x6w2h00v7lz")))) (properties `((upstream-name . "ChIPexoQual"))) (build-system r-build-system) (propagated-inputs @@ -11115,14 +11372,14 @@ penalized least squares regression method.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.72.3") + (version "1.74.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "1kxzrny19dqd9pqj27vzr15i071sl8ivznpfd6zlqhcymlcsq7nw")))) + "1bj87ksvch5cm5zxwgfiiql0j94pvzbpn59wp6bacyip65z7w3ax")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -11213,14 +11470,14 @@ and regression inferences from RNA-sequencing data.") (define-public r-ebseq (package (name "r-ebseq") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBSeq" version)) (sha256 (base32 - "1gh1cyb76gv2h0knh780648gsbgpn76adfj6x3pjzily5m5bmin0")))) + "0y23k607f61csj2ciaqnl8pzsjisqlcnnhlasv36446n8f3silx5")))) (properties `((upstream-name . "EBSeq"))) (build-system r-build-system) (propagated-inputs @@ -11235,13 +11492,13 @@ gene and isoform level using RNA-seq data") (define-public r-karyoploter (package (name "r-karyoploter") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "karyoploteR" version)) (sha256 (base32 - "1dcxq3651903wwzr7bww8c4wd8h5h7rklnqfgklqpss0psx59d2w")))) + "1nqcm2jlazm8wsa4p6a59m1j8y1qdwg0w3kii4dqnkann3q2q68x")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -11273,14 +11530,14 @@ coordinates.") (define-public r-lpsymphony (package (name "r-lpsymphony") - (version "1.26.3") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lpsymphony" version)) (sha256 (base32 - "0iqc6km4pw50li2q35km8jpa0p3i6a6way910wcz56yd2jjbjyz5")))) + "096d0dql1cg85mmxba3dy2a7ba3sxqphsviqqvx1n35xiidsnpyp")))) (build-system r-build-system) (arguments (list @@ -11312,14 +11569,14 @@ to install interface to SYMPHONY.") (define-public r-ihw (package (name "r-ihw") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IHW" version)) (sha256 (base32 - "04vbf42bzqydf5mi4mqmcyh0xdx4phs4cjhsm6fimhmjhxm8jyry")))) + "0i4yahgkrg9rnc0xldm026k6bd1bn5nkgkaf6kpyyday41rxzyq8")))) (properties `((upstream-name . "IHW"))) (build-system r-build-system) (propagated-inputs @@ -11341,14 +11598,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "0mh7arn5rv26picz05ywil5ynras91xv6diwh47s9ip75vp9s3cy")))) + "1dirwfmjl15lqh1dx1yhaqbfiz5iwzp03d3g64iy31nzi8sha4qq")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -11378,14 +11635,14 @@ interactive exploration of results.") (define-public r-residualmatrix (package (name "r-residualmatrix") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ResidualMatrix" version)) (sha256 (base32 - "0zqifr1zhsfhrkjlp0ajqiqc9f96yz8zr13yhl19lvw30pwg9rj9")))) + "1yay0i0nh2ax35ayqlpnmq0839syl5991hacyrbv3li3gqjc9qqv")))) (properties `((upstream-name . "ResidualMatrix"))) (build-system r-build-system) @@ -11407,14 +11664,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.14.1") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1yj84ba6px14hbqg8526527vfcxmzvmly34f7hba4vybdm1jscfm")))) + "1cswij2mdjsdh99rmyh68wscg6h7cs0cff69gnki4gzzjfxy8x3f")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -11450,14 +11707,14 @@ the numbers of cells across batches.") (define-public r-mast (package (name "r-mast") - (version "1.24.1") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MAST" version)) (sha256 (base32 - "1c0lc4abnb859x481ky6d3kc9zzxwvf4kqgwxyqapc4g72b4vh65")) + "0vm7v2anbrci6mcans9y9svd6xjm4waf2kny3rz0cjgsasw60ycx")) (snippet '(delete-file "docs/jquery.sticky-kit.min.js")))) (properties `((upstream-name . "MAST"))) @@ -11478,6 +11735,7 @@ the numbers of cells across batches.") r-biocgenerics r-data-table r-ggplot2 + r-matrix r-plyr r-progress r-reshape2 @@ -11506,14 +11764,14 @@ single cell assay data.") (define-public r-monocle (package (name "r-monocle") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "monocle" version)) (sha256 (base32 - "1d3xgh9xgqa28bgyd06zkjmg75lq7hdah3d140l1bqq2ii1bv62g")))) + "05pix638s4hkig2i048m5jjhvw6cqr2b5qvfkk14i64p9kpifmqj")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -11691,14 +11949,14 @@ user-defined and/or data-driven sets of hypotheses.") (define-public r-noiseq (package (name "r-noiseq") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "NOISeq" version)) (sha256 (base32 - "1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2")))) + "0cxhy4yrww6bh4z603389fikhix8rhfy04ylhm74fdmdng4jblg6")))) (properties `((upstream-name . "NOISeq"))) (build-system r-build-system) (propagated-inputs @@ -11717,14 +11975,14 @@ assumptions.") (define-public r-scdd (package (name "r-scdd") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scDD" version)) (sha256 (base32 - "0kmnmlzww2xfd04lp9nsh0wkigab9ipgqlsn2jrd77fizpd0kvwg")))) + "1ndb1zcbdy00xkfx18slrm5bnld9ci5scysc37clhsq2lq5xb25z")))) (properties `((upstream-name . "scDD"))) (build-system r-build-system) (propagated-inputs @@ -11755,14 +12013,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "0pg09r28xqjlvb6nbswglnmwi05q63fag6rp3sw41g6z8gm5wap7")))) + "0v3rd2h0n52qz9kqxa3l49rjfssfk252dy7j2nvi34y85win2p1w")))) (build-system r-build-system) (propagated-inputs (list r-aroma-light @@ -11799,14 +12057,14 @@ high-throughput analyses.") (define-public r-geoquery (package (name "r-geoquery") - (version "2.66.0") + (version "2.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GEOquery" version)) (sha256 (base32 - "0ck2aml1kxdahwcszi3j7hcikwi8fdnzphlrsn3h2q4dkk5x00kn")))) + "1xyrfj8b7j2wdjlbmwhx1c0hfbvr7l7jxyw2v64fbw8604zprv4s")))) (properties `((upstream-name . "GEOquery"))) (build-system r-build-system) (propagated-inputs @@ -11834,14 +12092,14 @@ the bridge between GEO and BioConductor.") (define-public r-illuminaio (package (name "r-illuminaio") - (version "0.40.0") + (version "0.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "illuminaio" version)) (sha256 (base32 - "1cw526mbhh0czkwk99qnr6hfwi4k4xi2bm5p14kw9sr00if59x12")))) + "190i3b9qmh26bic1lzi54mw4p1nrg57qijl1pg6b29w3i6srq692")))) (build-system r-build-system) (propagated-inputs (list r-base64)) @@ -11855,14 +12113,14 @@ files, including IDAT.") (define-public r-siggenes (package (name "r-siggenes") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "siggenes" version)) (sha256 (base32 - "0gis34s56y4xa61a9gywjwgd6525ywasa6r4xxhj3rshh1dz5jkv")))) + "0h5asj2w4xgfj9xapjawmxldnhq789py39drlr8illyhcczkzkbz")))) (build-system r-build-system) (propagated-inputs (list r-biobase r-multtest r-scrime)) @@ -11879,14 +12137,14 @@ Bayes Analyses of Microarrays} (EBAM).") (define-public r-bumphunter (package (name "r-bumphunter") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bumphunter" version)) (sha256 (base32 - "0jwbhd2fhm1w5slwhz8krnw835a8qb4akm3n3pv867bvi0xnp3g2")))) + "1xghz87702fg9r6n1igygf4ybb8mw8ff0i02qkx9jmm6vmmfhv18")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -11913,13 +12171,13 @@ studies.") (define-public r-mia (package (name "r-mia") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mia" version)) (sha256 (base32 - "0yz88ggv6d5rccdwzixwg9y1bc4xysazlmv1ph88wxs8r6fcmync")))) + "1p78yacx0cgihva7m2n3vnll5w4b47vl98hy12pq9rnmhk6r591z")))) (properties `((upstream-name . "mia"))) (build-system r-build-system) (propagated-inputs @@ -11961,13 +12219,13 @@ summarization.") (define-public r-microbiome (package (name "r-microbiome") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "microbiome" version)) (sha256 (base32 - "1j3lrrz6yxfzsr037c0bbdhrs0ll7jg0mpcvk3iqdryi5rysnx0x")))) + "120wyjv2r9cbjgxbp70nzf249hai8cqn59gcbgwnazynfy5ih1w8")))) (properties `((upstream-name . "microbiome"))) (build-system r-build-system) (propagated-inputs @@ -11995,16 +12253,50 @@ format and expands the available toolkit in order to facilitate the standardization of the analyses and the development of best practices.") (license license:bsd-2))) +;; This is a CRAN package but it depends on phyloseq, which is from +;; Bioconductor. +(define-public r-microbiomestat + (package + (name "r-microbiomestat") + (version "1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "MicrobiomeStat" version)) + (sha256 + (base32 + "1j5sar85a1gksc83pc4ypxwb0c7whxglx069zarphrgqfazcr1m4")))) + (properties `((upstream-name . "MicrobiomeStat"))) + (build-system r-build-system) + (propagated-inputs (list r-foreach + r-ggplot2 + r-ggrepel + r-lmertest + r-mass + r-matrix + r-matrixstats + r-modeest + r-phyloseq + r-statmod)) + (home-page "https://cran.r-project.org/package=MicrobiomeStat") + (synopsis "Statistical methods for microbiome compositional data") + (description + "This package provides a suite of methods for powerful and robust +microbiome data analysis addressing zero-inflation, phylogenetic structure and +compositional effects. The methods can be applied to the analysis of +other (high-dimensional) compositional data arising from sequencing +experiments.") + (license license:gpl3))) + (define-public r-milor (package (name "r-milor") - (version "1.6.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "miloR" version)) (sha256 (base32 - "07p9rs1jmgxqaahjbrnvvs94c142n2qfw8ip3qqkr6mhzwr19ly3")))) + "073s239aqkixsrarqxfv4nmpcj025k32nhql63qaxrkrvvdd34di")))) (properties `((upstream-name . "miloR"))) (build-system r-build-system) (propagated-inputs @@ -12046,14 +12338,14 @@ model.") (define-public r-minfi (package (name "r-minfi") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minfi" version)) (sha256 (base32 - "15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc")))) + "18b9yg9hnnm1saaiprm2hj86aajjwm1zwvpj0yadfa3s811pw4nq")))) (build-system r-build-system) (propagated-inputs (list r-beanplot @@ -12097,14 +12389,14 @@ methylation arrays.") (define-public r-methylumi (package (name "r-methylumi") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylumi" version)) (sha256 (base32 - "07kfyv3kkayzh0akxfl3p9gckw8qiplkxbyxw8npc7cb03ihgmc4")))) + "1aa0pwjyp2p9a4mx4n4qw88ndgrj56p669yzdkd7hxhc3x55nzlf")))) (build-system r-build-system) (propagated-inputs (list r-annotate @@ -12141,17 +12433,40 @@ background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.") (license license:gpl2))) +(define-public r-lefser + (package + (name "r-lefser") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "lefser" version)) + (sha256 + (base32 + "0wi70b4k7s0xj7bh46s0x0fckqc5qspzq8k4k913vg6cnhqgw2dd")))) + (properties `((upstream-name . "lefser"))) + (build-system r-build-system) + (propagated-inputs (list r-coin r-ggplot2 r-mass r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/waldronlab/lefser") + (synopsis "LEfSE method for microbiome biomarker discovery") + (description + "Lefser is an implementation in R of the popular \"LDA Effect +Size\" (LEfSe) method for microbiome biomarker discovery. It uses the +Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis +to find biomarkers of groups and sub-groups.") + (license license:artistic2.0))) + (define-public r-lumi (package (name "r-lumi") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "lumi" version)) (sha256 (base32 - "1091458is69dxnjrcd11czqy55c68sdnkrmpvlm6hw2cbghs2bjq")))) + "1lxxqr7x9jdjrsj5j95jb0dbd7p208vifxw3j4s4140zh1ppxnpj")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -12183,14 +12498,14 @@ especially Illumina Infinium methylation microarrays.") (define-public r-linnorm (package (name "r-linnorm") - (version "2.22.2") + (version "2.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Linnorm" version)) (sha256 (base32 - "0snsvyy8d85panizm848mrmjpgyc06iqp39d19rny3fphq3adwn5")))) + "1sqkmjah2lxahnvwv04a970za2b8kzvmxnb41k9xrnvj0akigc2d")))) (properties `((upstream-name . "Linnorm"))) (build-system r-build-system) (propagated-inputs @@ -12244,14 +12559,14 @@ evaluation of DEG analysis methods.") (define-public r-ioniser (package (name "r-ioniser") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "IONiseR" version)) (sha256 (base32 - "1xkxqavhcw22lhij87cpd5ps1ldkzzi0pp93d38pxbbhj15gc3d3")))) + "1yrsd5n9zam6wslc6savfn122v3wzzcc46w20mb849qq2np4frf0")))) (properties `((upstream-name . "IONiseR"))) (build-system r-build-system) (propagated-inputs @@ -12340,13 +12655,13 @@ published results; and a routine for graphical display.") (define-public r-tradeseq (package (name "r-tradeseq") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tradeSeq" version)) (sha256 (base32 - "0wkbjhwqk094nd5h6sl2nw5jp5vmkh9why635l8qkqmxa2jm3gh0")))) + "14b90x9h34mhbc4sdpzkygrrswf84pi1ddwpzxhvlvr9gs443xqs")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -12409,14 +12724,14 @@ peak definition in combination with known profile characteristics.") (define-public r-varianttools (package (name "r-varianttools") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantTools" version)) (sha256 (base32 - "181igcmlyx3ddmhml9wqcgw6ffdrqpmg4imd6ipf68c90agdgaz0")))) + "1vkdw626r1ffdsvry6qwhd1i3lkyb9wzrp9zf3dfafi02cap6r47")))) (properties `((upstream-name . "VariantTools"))) (build-system r-build-system) (propagated-inputs @@ -12449,14 +12764,14 @@ gmapR.") (define-public r-heatplus (package (name "r-heatplus") - (version "3.6.0") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Heatplus" version)) (sha256 (base32 - "0zbjw9f616dz1fpp6q6whbmlrf2gypq8pp9i66c376cs2aifp1si")))) + "031f25w960jp5nhd78v3iv6pib266cpbawhi9rrd7csw89vnswfx")))) (properties `((upstream-name . "Heatplus"))) (build-system r-build-system) (propagated-inputs @@ -12474,14 +12789,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "14wc7qgk1psknld05246cn0nqxpbjprax7j75h5yyd0w7hjyly2s")))) + "1pg86z4vbrp59kpq7zpscnjw9cgfkdqjrdp9zjvdf3xghgjvwl9a")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -12501,14 +12816,14 @@ sets of GO terms, gene products and gene clusters.") (define-public r-anota (package (name "r-anota") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "anota" version)) (sha256 (base32 - "1a9xgcp48zjql6an3kiv8li4saw10k1dl7qzyyw84xvx856ilv97")))) + "0ic12p1qyfrmh3l1wv7s9yi8sr84crj4nksmcx0lybb6rak9gy0x")))) (build-system r-build-system) (propagated-inputs (list r-multtest r-qvalue)) @@ -12553,13 +12868,13 @@ phenotype of interest.") (define-public r-fcscan (package (name "r-fcscan") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fcScan" version)) (sha256 - (base32 "0z83ncjxw9x8nvc6pncrvpf6lmamvgrv56j96s1f0x9jydk18chy")))) + (base32 "071sylwwj27bk39pkn5a29r7bmfpmyaixkkg7dqcdq230c1dsrps")))) (properties `((upstream-name . "fcScan"))) (build-system r-build-system) (propagated-inputs @@ -12586,14 +12901,14 @@ presence of additional sites within the allowed window size.") (define-public r-fgsea (package (name "r-fgsea") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fgsea" version)) (sha256 (base32 - "1frl5mchbrgqyxxdlw76qqq5i8vv2fdmy8xl8h8c8cvvmlz393qk")))) + "0chnrwiwk31crrx4am1yrbxjdqd3jycgjgczqzj7lxaa9v7lvm7z")))) (build-system r-build-system) (propagated-inputs (list r-bh @@ -12603,7 +12918,8 @@ presence of additional sites within the allowed window size.") r-fastmatch r-ggplot2 r-matrix - r-rcpp)) + r-rcpp + r-scales)) (native-inputs (list r-knitr)) (home-page "https://github.com/ctlab/fgsea/") @@ -12618,14 +12934,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.24.2") + (version "3.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0scp6sgb1iwwfh7gdak4dxf1hb870745km9nc9hga8pnsnqi5v3g")))) + "1whvgzw8p0nm3kchdndrxj4x3fhmq0vgbz77d54sqq1qri4j35qx")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -12653,14 +12969,14 @@ data.") (define-public r-enrichplot (package (name "r-enrichplot") - (version "1.18.4") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "enrichplot" version)) (sha256 (base32 - "1642yc2rw2c023bkz26y3kvmvg8badrc4vfx890mvsa70in2mi89")))) + "10vmlw58hgzcpv2hlxk9ircza889vs9z01z575633qj0ivsczh0z")))) (build-system r-build-system) (propagated-inputs (list r-aplot @@ -12693,14 +13009,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.6.2") + (version "4.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "017wqd1nwcrhbpzvhcqc3if0n084dspq7y3fbc5dnik6yi04q0dg")))) + "1vcqzk5a2y3g2vv5vlpvcpd45xdq6rs5djnrdkww536cwkas9zvy")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -12731,13 +13047,13 @@ profiles (GO and KEGG) of gene and gene clusters.") (define-public r-clusterexperiment (package (name "r-clusterexperiment") - (version "2.18.2") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterExperiment" version)) (sha256 (base32 - "03flqixy6flaqynpaf3nz42kwf71v53wxs5vywj3bqmninzywmbk")))) + "0h22zh6jpd2wsh6b9rnrmx8897aqlrsnw82kwphx8lay4r1vv706")))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -12777,14 +13093,14 @@ expression data sets.") (define-public r-mlinterfaces (package (name "r-mlinterfaces") - (version "1.78.0") + (version "1.80.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MLInterfaces" version)) (sha256 (base32 - "0xnaghm65ydk01gzx5g38jyq7vfdw206c2w59k0qg8lhy9fqky9x")))) + "1s5b27n01crfzrpshhiv6g0q0qf0dip1gw4nkrkg5sh5x9dsikq6")))) (properties `((upstream-name . "MLInterfaces"))) (build-system r-build-system) (propagated-inputs @@ -12809,6 +13125,7 @@ expression data sets.") r-shiny r-summarizedexperiment r-threejs)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/MLInterfaces/") (synopsis "Interfaces to R machine learning procedures") (description @@ -12820,14 +13137,14 @@ data in R and Bioconductor containers.") (define-public r-annaffy (package (name "r-annaffy") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annaffy" version)) (sha256 (base32 - "0qxihlhx7ijspvgzdp8zxzrc44y9pwkygvsllh4v47p85ham49fg")))) + "0jy3qk31lb11bixncb2w2hw1ibvik31bfi2l5vyq5wjyxndfyax6")))) (build-system r-build-system) (arguments `(#:phases @@ -12852,14 +13169,14 @@ It allows searching of biological metadata using various criteria.") (define-public r-a4core (package (name "r-a4core") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Core" version)) (sha256 (base32 - "0plgfzsvg220v6k6p0g7izsfw2lj78331lqyvz0p9vd91ynwp41k")))) + "14q9q3dxnmmm491af53hd0dwwqiz47xxrwy05axh85x4fh01j3xx")))) (properties `((upstream-name . "a4Core"))) (build-system r-build-system) (propagated-inputs @@ -12876,14 +13193,14 @@ arrays.") (define-public r-a4classif (package (name "r-a4classif") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Classif" version)) (sha256 (base32 - "0lirj0qzzrm996g8yh30x61cg1qkh436qd8xzgv3y3y3n5jj5d3w")))) + "1z5xypz5jvb06pk71x6953iirhh1w1mggm0pxqibg0ag9lx2zzmv")))) (properties `((upstream-name . "a4Classif"))) (build-system r-build-system) (propagated-inputs @@ -12906,14 +13223,14 @@ Affymetrix arrays.") (define-public r-a4preproc (package (name "r-a4preproc") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Preproc" version)) (sha256 (base32 - "00xs1vayl8v6in79iv7lwbn52yyyq4lv6k3k727g7il8x17mi8i0")))) + "1dxh0zbv4z4gqnwbv7yn247gx7cqv68vb43p6f98c2kyqilfpjg9")))) (properties `((upstream-name . "a4Preproc"))) (build-system r-build-system) (propagated-inputs @@ -12930,14 +13247,14 @@ is used for preprocessing the arrays.") (define-public r-a4reporting (package (name "r-a4reporting") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Reporting" version)) (sha256 (base32 - "09q8ng5kp47bqpj7m2y2112fkjxcnhzxk9v80hqksm8h1df46riv")))) + "0lx7fx2vlpq3c347gx842qlcvnzl0r25i5a55l0qbf8rb5liq2yv")))) (properties `((upstream-name . "a4Reporting"))) (build-system r-build-system) (propagated-inputs @@ -12954,14 +13271,14 @@ provides reporting features.") (define-public r-a4base (package (name "r-a4base") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4Base" version)) (sha256 (base32 - "14diri7gswd6h5p3bdhh20fy7i54d270mq985qcdvdyhx4kpw6g6")))) + "01c8rps321820b0pchfqv8shglb26rys7hqkwygpzzx3jj310v8x")))) (properties `((upstream-name . "a4Base"))) (build-system r-build-system) (propagated-inputs @@ -12985,14 +13302,14 @@ Affymetrix arrays.") (define-public r-a4 (package (name "r-a4") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "a4" version)) (sha256 (base32 - "1sis4hwrxyn2x96yysz82gffl2kkj68ry945y15zwikwk80s31hb")))) + "0n49scwwmg51gcakbc0bfjcy1lcpdxg974l11yk35kj0bg9ynpgi")))) (build-system r-build-system) (propagated-inputs (list r-a4base r-a4classif r-a4core r-a4preproc r-a4reporting)) @@ -13006,14 +13323,14 @@ Affymetrix arrays.") (define-public r-abseqr (package (name "r-abseqr") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "abseqR" version)) (sha256 (base32 - "1z5an4vsm55a0qr46qmp8562vc3xdam5f3840r8hcdnn5dvzw414")))) + "05kcwmv3d59lrdnpi82701biwawnnpfvpwr170xdi3hfdff6g59c")))) (properties `((upstream-name . "abseqR"))) (build-system r-build-system) (inputs @@ -13054,14 +13371,14 @@ further downstream analysis on its output.") (define-public r-bacon (package (name "r-bacon") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bacon" version)) (sha256 (base32 - "1v5kvvbc5fwvs84d2aq6gq6f6z0l68n7626gcnc8mh3sc27lxz53")))) + "1h2yh85c6d4j2abdh5l7m6zcxh9i5xzrwwjkwas4nfs48h74z293")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel r-ellipse r-ggplot2)) @@ -13079,14 +13396,14 @@ fitting a three-component normal mixture on z-scores.") (define-public r-rgadem (package (name "r-rgadem") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGADEM" version)) (sha256 (base32 - "070i3jdq8b5w7k42xw2fc3vcmv312i19fa1am4fbk3g3ssnm61p3")))) + "08li2wql2zhg06z0rjws9qcnv3ishgnpc6k8xyjcf7yfyg7qpk1d")))) (properties `((upstream-name . "rGADEM"))) (build-system r-build-system) (propagated-inputs @@ -13133,12 +13450,12 @@ distributions, modules and filter motifs.") (define-public r-motifdb (package (name "r-motifdb") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MotifDb" version)) (sha256 - (base32 "122ifxmbi0v3192cd9chq265i3dyw3hzwsndq3w97f4d68vll7gl")))) + (base32 "18d0qj9sn4bhfjy2mwsz2nnm41xlsqjslsv69nkhv19w9zd842pw")))) (properties `((upstream-name . "MotifDb"))) (build-system r-build-system) (propagated-inputs @@ -13150,7 +13467,7 @@ distributions, modules and filter motifs.") r-s4vectors r-splitstackshape)) (native-inputs - (list r-knitr)) + (list r-formatr r-knitr r-markdown r-rmarkdown)) (home-page "https://www.bioconductor.org/packages/MotifDb/") (synopsis "Annotated collection of protein-DNA binding sequence motifs") (description "This package provides more than 2000 annotated position @@ -13160,12 +13477,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.12.3") + (version "2.13.7") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "073xv26yaksqa0j2vyqf8ak5yqsxg5s86izdlmlwdidnxdnd16si")))) + (base32 "0j4i3059n0g9n73nyxaca7pd4hncvgp0ww63i3kyp5pnvwycsax2")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -13210,16 +13527,40 @@ Bioconductor.") (define-public r-motifstack (package (name "r-motifstack") - (version "1.42.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "motifStack" version)) (sha256 (base32 - "18gfx5dq83s2ny39a7cgg4r3b05gg9l0kfg83brwrm1cby08jdhm")))) + "1g46cxn1h3cqr0yrj6ancshzygiqr9finf1vmmig3h9g0ijgr5lz")) + (snippet + '(delete-file "inst/htmlwidgets/lib/d3/d3.v4.min.js")))) (properties `((upstream-name . "motifStack"))) (build-system r-build-system) + (arguments + (list + #:modules '((guix build utils) + (guix build r-build-system) + (srfi srfi-1)) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "inst/htmlwidgets/lib/d3" + (call-with-values + (lambda () + (unzip2 + `((,(assoc-ref inputs "_") + "d3.v4.min.js")))) + (lambda (sources targets) + (for-each (lambda (source target) + (format #true "Processing ~a --> ~a~%" + source target) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))) + sources targets))))))))) (propagated-inputs (list r-ade4 r-biostrings @@ -13228,7 +13569,14 @@ Bioconductor.") r-tfbstools r-xml)) (native-inputs - (list r-knitr)) + (list esbuild r-knitr + (origin + (method url-fetch) + (uri "https://web.archive.org/web/20230428092426id_/\ +https://d3js.org/d3.v4.js") + (sha256 + (base32 + "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))) (home-page "https://bioconductor.org/packages/motifStack/") (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") (description @@ -13242,14 +13590,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "1sz0gmwc5iam83pxnc702pd5h6nsa46kb0wsqs8ysb1ximbkfh5h")))) + "1z8h9sbr6xqwbsfisr33qdxg0xdrw8r4vvxl1pf4x8vv08zw0vx6")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -13280,14 +13628,14 @@ position-specific scores within R and Bioconductor.") (define-public r-atacseqqc (package (name "r-atacseqqc") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ATACseqQC" version)) (sha256 (base32 - "12ggi2dzf8qyzjrxprvk099f61yrabg2d84iqnjxzrn77v6z19b2")))) + "0mcrkmirss484d2mskikyjdz5cmbhdk52yxkffz9g8g5m9lkq5xk")))) (properties `((upstream-name . "ATACseqQC"))) (build-system r-build-system) (propagated-inputs @@ -13327,14 +13675,14 @@ footprints.") (define-public r-gofuncr (package (name "r-gofuncr") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOfuncR" version)) (sha256 (base32 - "0d0xis4nns5icsr16w4ik2d95n3p2h93c47jvlp22crv7f4rlaa5")))) + "05509xf768x8asqadjj5s50m0yqnklrxi28bmqd22cn6cbmahszw")))) (properties `((upstream-name . "GOfuncR"))) (build-system r-build-system) (propagated-inputs @@ -13432,14 +13780,14 @@ different identifieres using the Biocore Data Team data-packages (e.g. (define-public r-annotationtools (package (name "r-annotationtools") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotationTools" version)) (sha256 (base32 - "1z5vgblhi1kj2n9d4kbqgvwnm48372q0szgjshch8g39dypijvhd")))) + "0dwbh2h2mp8gy0kwqmkri3q2glnzcj8cn83j1qyh7lk15anc33g8")))) (properties `((upstream-name . "annotationTools"))) (build-system r-build-system) @@ -13457,14 +13805,14 @@ text files).") (define-public r-allelicimbalance (package (name "r-allelicimbalance") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AllelicImbalance" version)) (sha256 (base32 - "0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263")))) + "1ms3x3x2gvhgllff3nwawg5jlpmgx6dhwll0dghklnv3lssbx4c7")))) (properties `((upstream-name . "AllelicImbalance"))) (build-system r-build-system) @@ -13500,14 +13848,14 @@ investigation using RNA-seq data.") (define-public r-aucell (package (name "r-aucell") - (version "1.20.2") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AUCell" version)) (sha256 (base32 - "1qb13qd5xzgrpx6jlg3ll0ff5spz3y06ji31vvqzm759almg2w3s")))) + "1zqjmg8nxxj30lxppl685ihynbz44vw7qm3kwjq6cp83c5556hz9")))) (properties `((upstream-name . "AUCell"))) (build-system r-build-system) (propagated-inputs @@ -13541,14 +13889,14 @@ needed.") (define-public r-ebimage (package (name "r-ebimage") - (version "4.40.1") + (version "4.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBImage" version)) (sha256 (base32 - "08hsfxfqfznfqnpl2vygry7xn6npjpibswy4qi6zmvifdarx6i1j")))) + "0z0ajmy1zx7mqcjm2ibyk2qg3cj00kl76padyksbdbmwdncxs8yb")))) (properties `((upstream-name . "EBImage"))) (build-system r-build-system) (propagated-inputs @@ -13580,14 +13928,14 @@ visualization with image data.") (define-public r-yamss (package (name "r-yamss") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yamss" version)) (sha256 (base32 - "0bh06mncjrkihz2j29hasbipfl50x7393wshdcnlxrs5rrq73r0n")))) + "0kjlp62s2393jdwp0crizsgp4iqagbgnd3hdl9vpbr9qrjxg4s7m")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -13613,14 +13961,14 @@ analysis.") (define-public r-gtrellis (package (name "r-gtrellis") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gtrellis" version)) (sha256 (base32 - "09f20qam59iwr48g854b7ydbsbqy90mdy83i2i0am4gybv5isgqg")))) + "1kk7ysscq8xdbn35b20s8sn8gl93sy0c718fmvr1yrhiqaxq5alr")))) (build-system r-build-system) (propagated-inputs (list r-circlize r-genomicranges r-getoptlong r-iranges)) @@ -13639,14 +13987,14 @@ genomic categories and to add self-defined graphics in the plot.") (define-public r-somaticsignatures (package (name "r-somaticsignatures") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SomaticSignatures" version)) (sha256 (base32 - "0xyh4pwwbpa1bmamqdhp84qhjdc2qsxc43xgknjrrja24d06ji2j")))) + "075w88x7lv2fkp2ipqgxp4pzh6kbjw3nmp0qra2p4fss4j3g8d6s")))) (properties `((upstream-name . "SomaticSignatures"))) (build-system r-build-system) @@ -13678,14 +14026,14 @@ decomposition algorithms.") (define-public r-yapsa (package (name "r-yapsa") - (version "1.24.0") + (version "1.25.0") (source (origin (method url-fetch) (uri (bioconductor-uri "YAPSA" version)) (sha256 (base32 - "17yxzqvyaa423k0rskahlgqxcsi70flgsxniry3f4m8yvmghxxkz")))) + "0xva7vljq2k78rzjnjlp4x3ylwk86jaqn2cgbff4h4sb8rfdya7c")))) (properties `((upstream-name . "YAPSA"))) (build-system r-build-system) (propagated-inputs @@ -13727,14 +14075,14 @@ provided.") (define-public r-gcrma (package (name "r-gcrma") - (version "2.70.0") + (version "2.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gcrma" version)) (sha256 (base32 - "0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1")))) + "0k4fsmqkv82d3a6v3gwphvbri5sgbd3f1s4qyv960rhyk2xj2b4p")))) (build-system r-build-system) (propagated-inputs (list r-affy @@ -13809,14 +14157,14 @@ chips with the MAQC reference datasets.") (define-public r-quantro (package (name "r-quantro") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "quantro" version)) (sha256 (base32 - "0f274wh0w6nyipac05y6s2m2p60vkls5j4fwa5bc419j68h4znnz")))) + "08m94q65c11isbkx9xljm2bx2aq2rml1bqh5i1cg81xg2ilm9h6a")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -13842,14 +14190,14 @@ groups.") (define-public r-yarn (package (name "r-yarn") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "yarn" version)) (sha256 (base32 - "0sqbll7ja0qr8r28dqmydmkvg4ijfm7z8hbrsrz3xxdan70bmd2r")))) + "0ddfl4jp0n8sb665hcpsij959fl28rj22n1h61wp2374kpc0fwfj")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -13879,14 +14227,14 @@ large RNA-seq experiments.") (define-public r-roar (package (name "r-roar") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "roar" version)) (sha256 (base32 - "1bf3ii3zaxkzw5y1wc5c474bq4cgavb67df54czmd3zi1lbhzphd")))) + "0p5q6nyp8d0gl95rd89xrs08gv87m1q6d0x4ws2b6sd4gc1nw2ny")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics @@ -13947,14 +14295,14 @@ genes.") (define-public r-massspecwavelet (package (name "r-massspecwavelet") - (version "1.64.1") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MassSpecWavelet" version)) (sha256 (base32 - "0p8cd4r3c8va5gybs1vlm3kn7jcg1xg529hvvg27fybb3g91nvqg")))) + "1nc1imxia71sxxvi77f91yhwxza2l8kk1d7zkp5680xzw6yd6ajr")))) (properties `((upstream-name . "MassSpecWavelet"))) (build-system r-build-system) @@ -13971,14 +14319,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.20.0") + (version "3.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "1gj0nd90c6ykwn1n7xndzrgfv5dzy0y2lh3bf8120nacccgxl2qx")))) + "112g2lpi074cr8g09cqwjbcwv9aw4djr7ashxpnxjycd3ayc0j3v")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -13990,6 +14338,7 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") r-mscoreutils r-msfeatures r-msnbase + r-multtest r-mzr r-plyr r-protgenerics @@ -14012,13 +14361,13 @@ data for high-throughput, untargeted analyte profiling.") (define-public r-wppi (package (name "r-wppi") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wppi" version)) (sha256 (base32 - "0kc3nkim8fhajhai5bwzwirsg74zbdib3dd7cfr75ddwd8myc913")))) + "06y4pq8msjzwrw1jgyj9yskgpfhvcz54qcsv0h14bakhyrwk00pg")))) (properties `((upstream-name . "wppi"))) (build-system r-build-system) ;; This is necessary because omnipathr attempts to write a configuration @@ -14053,14 +14402,14 @@ scores and a path search algorithm.") (define-public r-wrench (package (name "r-wrench") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Wrench" version)) (sha256 (base32 - "0n7mvj9jdp8w5w64i49kkqzbrvpv2vzx6y6fb7g2sqp24wqrn39x")))) + "18x12395928d0mf8kffmdjqkdxrzgqzzhhvs7sdzldwyas6hfg2h")))) (properties `((upstream-name . "Wrench"))) (build-system r-build-system) (propagated-inputs @@ -14077,14 +14426,14 @@ that arising from 16s metagenomic surveys.") (define-public r-wiggleplotr (package (name "r-wiggleplotr") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wiggleplotr" version)) (sha256 (base32 - "1yp9siy4249wkwd0yy5lkwp79xir53f8mihiv4dkir8fscgampl3")))) + "15gbs10bi1alxxbxaj4h3hzfgck4nxygy896y34x81w1rn7in3vp")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -14111,14 +14460,14 @@ visualization of exonic read coverage.") (define-public r-widgettools (package (name "r-widgettools") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "widgetTools" version)) (sha256 (base32 - "1p93dzf7w9z1ria0f8n32aymam9abxyg50ngnh7s6a8n24mvvjy5")))) + "03bvh2jk97jj40z35q5n1is2wxrs4dggw08ndyywy4pzx1diqdc4")))) (properties `((upstream-name . "widgetTools"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/widgetTools/") @@ -14132,14 +14481,14 @@ widgets in R.") (define-public r-webbioc (package (name "r-webbioc") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "webbioc" version)) (sha256 (base32 - "1mgag0gjavpld4xxlpfafq6fhzjafxgqyf677xrm6ff26z6z1ja2")))) + "0z2sixzs0rwdwdhxs5mqzghgiw4g64l8p9ag5lw289bzs4c4kqnd")))) (build-system r-build-system) (inputs (list netpbm perl)) @@ -14164,14 +14513,14 @@ Currently only Affymetrix oligonucleotide analysis is supported.") (define-public r-zinbwave (package (name "r-zinbwave") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zinbwave" version)) (sha256 (base32 - "1356ms5y6fg7ndn8hvs6zsyr0jg6ah7a56qxd2x4xgyjj3xcakbv")))) + "1bmxbzpgmwama42a3vi1n0sic166v5zs0kl9mhmrh0rrx0nv303k")))) (build-system r-build-system) (propagated-inputs (list r-biocparallel @@ -14197,14 +14546,14 @@ the data.") (define-public r-zfpkm (package (name "r-zfpkm") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zFPKM" version)) (sha256 (base32 - "1wsmv4fld4s7l0qh84ghizq8k388ybdz9hzzis2gn1nn57q1c7wi")))) + "1fkzyq282xafyapgi5xi1c2dmfkyikqvf622pycjs80fas38044h")))) (properties `((upstream-name . "zFPKM"))) (build-system r-build-system) (propagated-inputs @@ -14222,14 +14571,14 @@ This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID (define-public r-rbowtie2 (package (name "r-rbowtie2") - (version "2.4.2") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie2" version)) (sha256 (base32 - "0cbm6q4v9ddyx4gnw2p47ssyhnmjfxahvzbzwjzn0my3ixssy0aj")))) + "11h4irhi0pxd0l378im455amqfamqypyl0ri2cs8nk1lg184ridr")))) (properties `((upstream-name . "Rbowtie2"))) (build-system r-build-system) (propagated-inputs @@ -14249,14 +14598,14 @@ rapid adapter trimming, identification, and read merging.") (define-public r-progeny (package (name "r-progeny") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "progeny" version)) (sha256 (base32 - "0f5sfi9r9dr6w3xmspsbzby8dpza8x7djif7p2h6l99kwkf68jsb")))) + "047x6by3xa15gvi3kny5pkqxaq8d2kzcfi55ic5j7a351715l6l7")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -14281,14 +14630,14 @@ expression\".") (define-public r-arrmnormalization (package (name "r-arrmnormalization") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ARRmNormalization" version)) (sha256 (base32 - "14mffjsy7cwpa2xf8zdqwdk6mnfj3lf06y8s59ndh531b45nw5wc")))) + "001nwl605prg942vmnbb1rwjwgpscpjs27ssic3h10rlmpb65yzp")))) (properties `((upstream-name . "ARRmNormalization"))) (build-system r-build-system) @@ -14304,14 +14653,14 @@ Infinium HumanMethylation 450k assay.") (define-public r-biocfilecache (package (name "r-biocfilecache") - (version "2.6.1") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocFileCache" version)) (sha256 (base32 - "16316a5pgyl5rppyviibf6z3k3m7xmvqyylf1kxdpg0avs6dk8w7")))) + "1qk1n50arlk0mfkv9p3zl3lqbapzfkjdbadv51hsp4h9lyaw9sbg")))) (properties `((upstream-name . "BiocFileCache"))) (build-system r-build-system) (propagated-inputs @@ -14321,7 +14670,6 @@ Infinium HumanMethylation 450k assay.") r-dplyr r-filelock r-httr - r-rappdirs r-rsqlite)) (native-inputs (list r-knitr)) @@ -14337,14 +14685,14 @@ and data files used across sessions.") (define-public r-iclusterplus (package (name "r-iclusterplus") - (version "1.34.3") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iClusterPlus" version)) (sha256 (base32 - "0d7qsdjry5avflrvgjj287xqn9dr54pqiqvpgywzdmdwn82m0dfp")))) + "1lbkmin9pkk9yzpmwrfyniyqnwmp0wcgiirq8prmzi5mvndl6wm3")))) (properties `((upstream-name . "iClusterPlus"))) (build-system r-build-system) (native-inputs (list gfortran)) @@ -14367,14 +14715,14 @@ Gaussian distributions.") (define-public r-rbowtie (package (name "r-rbowtie") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rbowtie" version)) (sha256 (base32 - "1kbpqhidj2bwhp9gxqx2qjaby6fc2dfrnnyjkciswgxckis6h2pc")))) + "1hfr1zdvikvygzgyy58f5rnz5jkmsrhwa930h331wx5012hhmnv7")))) (properties `((upstream-name . "Rbowtie"))) (build-system r-build-system) (arguments @@ -14403,14 +14751,14 @@ alignment tool.") (define-public r-sgseq (package (name "r-sgseq") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SGSeq" version)) (sha256 (base32 - "03ddz0mpgqqb52r7wa46bcr1ybf40126pg0n0n0pv6fnbq0ifwyc")))) + "0qsmy85400in2xvw3bnzjnk8ni3lipqjc81npk3fmvbp6cb85njq")))) (properties `((upstream-name . "SGSeq"))) (build-system r-build-system) (propagated-inputs @@ -14446,14 +14794,14 @@ interpretation.") (define-public r-rhisat2 (package (name "r-rhisat2") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhisat2" version)) (sha256 (base32 - "19dc9fadgl55icqc5xv834kigicxxr6cny83247jjbgf5zp16piv")))) + "1x9phnrk27v2r3ldqa9cd6yp2q3y5p2rm9wmra3wgrmhz9gxq1qy")))) (properties `((upstream-name . "Rhisat2"))) (build-system r-build-system) (arguments @@ -14484,14 +14832,14 @@ index.") (define-public r-quasr (package (name "r-quasr") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "QuasR" version)) (sha256 (base32 - "1pp94368aj5wx0zcnbbm6zrxrfhixmbcdzpj2lka3blvq5j7sncj")))) + "09k4r5a735022rc33k6a7pr98qxwy8ijsn451hcw18dimqzm78bx")))) (properties `((upstream-name . "QuasR"))) (build-system r-build-system) (propagated-inputs @@ -14526,14 +14874,14 @@ quantification of genomic regions of interest.") (define-public r-rqc (package (name "r-rqc") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rqc" version)) (sha256 (base32 - "02k64pjd1dlz5sksdbkbii9z4ihf1833ws7wwj81w3757zzabx0x")))) + "15w5bmcl7h3fz6qhdqz4qc3qkg3pxcmzapg4mnnckzmyg8kh0i4l")))) (properties `((upstream-name . "Rqc"))) (build-system r-build-system) (propagated-inputs @@ -14569,14 +14917,14 @@ graphics.") (define-public r-birewire (package (name "r-birewire") - (version "3.30.0") + (version "3.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiRewire" version)) (sha256 (base32 - "0nr40nm87qzbni3w0cik887csc899jh7j8z82i94v15fc30vfilh")))) + "1741raw1834093y5zhgx9jywfgz0wl0idlkynvab2c8vi40kc9a8")))) (properties `((upstream-name . "BiRewire"))) (build-system r-build-system) (propagated-inputs @@ -14622,14 +14970,14 @@ Markov-Chain-Monte-Carlo is applied to sample the activity states.") (define-public r-multidataset (package (name "r-multidataset") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiDataSet" version)) (sha256 (base32 - "1qja5xd42wh8qbcil4hhnmh9zlby2gfglax2qbf5bzg3h6yzpy4g")))) + "1qyvwhmdv27xsyljyzyh52pn6x0wqx8rslvr2j7vqcjyywv270x6")))) (properties `((upstream-name . "MultiDataSet"))) (build-system r-build-system) (propagated-inputs @@ -14659,14 +15007,14 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "0vjwci0z83b56q1wi1k00926f0vh3220a44m0zzfxg2cm5j3fwxb")))) + "1cq5ixaxag5r6nvl73c8bznxkdjhxw1r7qx90ml7qm4jr7wyi173")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -14701,14 +15049,14 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj")))) + "19sl75168zv6qqmgsfnhcyw1z0lp0phmky40lsl6bbmy4k2hfw38")))) (build-system r-build-system) (propagated-inputs (list r-biobase @@ -14736,14 +15084,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "08f3xikgb0z1j7n8i04yn1dlfj8rxc76nmf5b7i5ljcp0jqiv07n")))) + "1vjbk1vpqjxy9wv2a6sc32yyk0bhkbvdx9hl3vs5yjifwdswh2pw")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -14777,14 +15125,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.12.3") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "0lhmva8yghlbb44h1fvbcqfp8zvdn4pd4nwyd2drh6b271f8qjdd")))) + "1h1h0qrbd55p16d62v50nfan07vvnrbb9kjzpqfw0n8dc2xjwj1c")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -14803,13 +15151,13 @@ and to both short and long sequence reads.") (define-public r-flowai (package (name "r-flowai") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowAI" version)) (sha256 (base32 - "18zrlnjw89iglxhw65ys8x4r44pdzp5chrgwx7w44sh7yd8576g9")))) + "0ydy98qsiqpw0b6fvmlv09kza94qjcl40ma9pknzgbq21ac4z25g")))) (properties `((upstream-name . "flowAI"))) (build-system r-build-system) (propagated-inputs @@ -14869,14 +15217,14 @@ the quality control enables the detection and removal of anomalies.") (define-public r-consensusclusterplus (package (name "r-consensusclusterplus") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ConsensusClusterPlus" version)) (sha256 (base32 - "15cz3bbl21vzf5xn5xb791sy2yvzir7h4fdqm0a5anhbh8jg0iaq")))) + "0ig6xfhd70my5j4xrdy8srg1wi8nb3kcxlrld9py47psrq9vdadm")))) (properties `((upstream-name . "ConsensusClusterPlus"))) (build-system r-build-system) @@ -14935,14 +15283,14 @@ of the analyses while minimizing technical noise.") (define-public r-cytolib (package (name "r-cytolib") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "0rgqlqasil75b03c8c4nyg71ybysrsbqb0bwk6hbnaw8rljxdmi5")))) + "0r58960jhq44qs6p0l0kd4iazflxdar7sc7m2xa7dwwl9zh5zm42")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) (native-inputs @@ -14961,14 +15309,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj")))) + "1zkv4nwc6vg0jd4rh8mswdhr9cbq7ll98424hl5vs9hklal6kw8d")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -14993,14 +15341,14 @@ with flow cytometry data.") (define-public r-flowmeans (package (name "r-flowmeans") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowMeans" version)) (sha256 (base32 - "1hmr2i5svg1wvdgqhnp25k1c21p2pdd0ia9py5kp9sm5qvc9vngw")))) + "18lp1pickpd68fl7a4nidyvyh4yf53gbgn2f2yxaxfp2mk3mj88w")))) (properties `((upstream-name . "flowMeans"))) (build-system r-build-system) (propagated-inputs @@ -15016,23 +15364,22 @@ change point detection.") (define-public r-ncdfflow (package (name "r-ncdfflow") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ncdfFlow" version)) (sha256 (base32 - "0ak1rrd0r899nz4zdg9v3pkvlp94sbcc3q6xl249krgbx0a3sizm")))) + "0nrj4g02kx763wb70fzvhidmzp82gr1g3fp1aa1bv34cj4lnp47q")))) (properties `((upstream-name . "ncdfFlow"))) (build-system r-build-system) (propagated-inputs (list r-bh r-biobase r-biocgenerics + r-cpp11 r-flowcore - r-rcpp - r-rcpparmadillo r-rhdf5lib r-zlibbioc)) (native-inputs @@ -15047,14 +15394,14 @@ manipulation of flow cytometry data.") (define-public r-ggcyto (package (name "r-ggcyto") - (version "1.26.4") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggcyto" version)) (sha256 (base32 - "1pj1v0bhvckvwn1p826phskqz9lv71c1913cz5w0fd87dzdbpzpj")))) + "1b2xsn0avm6r4zylygdhab3zz3v8qvwbm1xr58894dwgysdk8zc5")))) (properties `((upstream-name . "ggcyto"))) (build-system r-build-system) (propagated-inputs @@ -15084,14 +15431,14 @@ statistics to the plot.") (define-public r-flowviz (package (name "r-flowviz") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowViz" version)) (sha256 (base32 - "0yz2b3l0bv5i7vrr893wrs3jl215i17m2hr92iisdc6mh9i0lpz8")))) + "0y16hzadpr5c99cwkphc07vh6lypgfk5nacbmn7mmrw01b3gbk67")))) (properties `((upstream-name . "flowViz"))) (build-system r-build-system) (propagated-inputs @@ -15115,14 +15462,14 @@ statistics to the plot.") (define-public r-flowclust (package (name "r-flowclust") - (version "3.36.1") + (version "3.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowClust" version)) (sha256 (base32 - "1r27nm5dxlhl5rk96dkjfx8326bvdgx55xg4w2zji3m49x9db2gs")))) + "1gmkmx6gzx4w39ijcad3lx2xnr2b833mhs8gcmc6k21k57aznzs2")))) (properties `((upstream-name . "flowClust"))) (build-system r-build-system) (arguments @@ -15149,14 +15496,14 @@ model with Box-Cox transformation.") (define-public r-rprotobuflib (package (name "r-rprotobuflib") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RProtoBufLib" version)) (sha256 (base32 - "07d5skr8cp0hyjbs7whw4h8scrf2w4hyn0wzj3khqdss53zmmr2m")))) + "0qlb3fp4lj3wys2hgrdrccfdf0lf85qnk0g117n959mg3y0dqikq")))) (properties `((upstream-name . "RProtoBufLib"))) (build-system r-build-system) (arguments @@ -15178,14 +15525,14 @@ for other R packages to compile and link against.") (define-public r-flowworkspace (package (name "r-flowworkspace") - (version "4.10.1") + (version "4.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowWorkspace" version)) (sha256 (base32 - "0jmbfclkfm0n2mshk94906kivii7awlskf7l7ydn8ki8wrpzxqg4")))) + "1ln98xnnqlz3hqdyhypzarw7jcghd5gjaw8h42yw41w0plhh4wyr")))) (properties `((upstream-name . "flowWorkspace"))) (build-system r-build-system) (propagated-inputs @@ -15225,14 +15572,14 @@ matches the flowJo analysis.") (define-public r-flowstats (package (name "r-flowstats") - (version "4.10.0") + (version "4.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "flowStats" version)) (sha256 (base32 - "10xq0rfnshvam2yh34566ywmsby44aa1fg8wqwmllm202rhcgl2p")))) + "13mdpdndalm0d6azjancw0xcbdc674ivkj8kp6ccfpdd7gydhr4j")))) (properties `((upstream-name . "flowStats"))) (build-system r-build-system) (propagated-inputs @@ -15263,14 +15610,14 @@ package.") (define-public r-opencyto (package (name "r-opencyto") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "openCyto" version)) (sha256 (base32 - "16wsa9dhnz8gz1siyhfxvnbfg142g7fmhxiqxr7n69qpq9w8yhr0")))) + "0z0p09mkap1jqlq1x33i2ik87pbhwq85xgqyfsx4r360nhv06pna")))) (properties `((upstream-name . "openCyto"))) (build-system r-build-system) (propagated-inputs @@ -15299,23 +15646,23 @@ sequential way to mimic the manual gating strategy.") (define-public r-cytoml (package (name "r-cytoml") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CytoML" version)) (sha256 (base32 - "105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa")))) + "19rlg15nk2205vma4whpqmvlazww5i3ibxhmk9cljsaj4ql560vf")))) (properties `((upstream-name . "CytoML"))) (build-system r-build-system) (inputs - (list libxml2 zlib)) + (list libxml2 #;zlib + )) (propagated-inputs - (list r-base64enc - r-bh + (list r-bh r-biobase - r-corpcor + r-cpp11 r-cytolib r-data-table r-dplyr @@ -15324,20 +15671,13 @@ sequential way to mimic the manual gating strategy.") r-ggcyto r-graph r-jsonlite - r-lattice r-opencyto - r-plyr r-rbgl - r-rcpp - r-rcpparmadillo - r-rcppparallel r-rgraphviz r-rhdf5lib r-rprotobuflib - r-runit r-tibble r-xml - r-xml2 r-yaml)) (native-inputs (list r-knitr)) @@ -15351,37 +15691,30 @@ standard to exchange gated cytometry data with other software platforms.") (define-public r-flowsom (package (name "r-flowsom") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FlowSOM" version)) (sha256 (base32 - "1s7xilhhc55igq0zmvpfzhnh5df8bzmm3daknz75xhzhhg5b7z1c")))) + "13y0ny61skj14mfhjwpa5zmflzdqxy2vf6gd4m9358g4wxfbhkv0")))) (properties `((upstream-name . "FlowSOM"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-colorramps r-consensusclusterplus - r-cytoml r-dplyr r-flowcore - r-flowworkspace r-ggforce r-ggnewscale r-ggplot2 - r-ggpointdensity r-ggpubr - r-ggrepel r-igraph r-magrittr - r-pheatmap - r-rcolorbrewer r-rlang r-rtsne - r-scattermore r-tidyr r-xml)) (home-page "https://bioconductor.org/packages/FlowSOM/") @@ -15394,14 +15727,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.22.0") + (version "6.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0w6shihvnvkjycba1hy8drd8wcxxcl2rimkrb4vdl8aygdifrarx")))) + "0dqndpmi56g772sra49vdrkjs4m9h2gzimwv3bwmw2l0krh2ax8s")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -15440,14 +15773,14 @@ delete entire rows with missing data.") (define-public r-depecher (package ;Source/Weave error (name "r-depecher") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DepecheR" version)) (sha256 (base32 - "1j4gxgw1s3a0nm888k02qi1smxqsplc42827ks666md025h9bxcj")))) + "1kn1w1fs19gjvg8nhbvj6hyp32h6k81dnal4ab12xl1jgaa3xj5p")))) (properties `((upstream-name . "DepecheR"))) (build-system r-build-system) (propagated-inputs @@ -15486,14 +15819,14 @@ data, to only emphasize the data that actually matters.") (define-public r-rcistarget (package (name "r-rcistarget") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RcisTarget" version)) (sha256 (base32 - "02lz2m2zhwy1dvmjvlss6qg0dh574qhnvn7al3wx7ck1hkz0dgi2")))) + "0dp2y85mfn995rvg698xnxlkz1kd8g0byjypxx62cpfldnkrinxl")))) (properties `((upstream-name . "RcisTarget"))) (build-system r-build-system) (propagated-inputs @@ -15528,14 +15861,14 @@ genes in the gene-set that are ranked above the leading edge).") (define-public r-chicago (package (name "r-chicago") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Chicago" version)) (sha256 (base32 - "1b24iiy6d5kzpixgpdkg4s1cb50jdrmgn9sjgvwr1qinckwz6zdn")))) + "04h4a5nyc78jlsg9pj8ay559bwb8y1nm80v9zvyxd7r490yn7k7s")))) (properties `((upstream-name . "Chicago"))) (build-system r-build-system) (propagated-inputs @@ -15574,14 +15907,14 @@ expression space.") (define-public r-cicero (package (name "r-cicero") - (version "1.16.2") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "cicero" version)) (sha256 (base32 - "1gf359x6lvm3kc4mlsh7vxf8lmvhp080fi0cksvb4mcypafp67cv")))) + "12zdygnwqjla99wzvvxzcmiwmh4v0rmnx4yix02gbj8xl4bxmm51")))) (build-system r-build-system) (propagated-inputs (list r-assertthat @@ -15641,14 +15974,14 @@ accessibility data.") (define-public r-circrnaprofiler (package (name "r-circrnaprofiler") - (version "1.12.2") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "circRNAprofiler" version)) (sha256 (base32 - "1i954hn7xyajpkg4fks04jd86flcmy2326nzpmxgy8h69jkzdc8q")))) + "0gagfm7v5bnnfj1zy6zf4cg91bj8nvv4vm38f3a1s4q2xc8pcvfj")))) (properties `((upstream-name . "circRNAprofiler"))) (build-system r-build-system) @@ -15776,14 +16109,14 @@ cisTopics and explore the nature and regulatory proteins driving them.") (define-public r-genie3 (package (name "r-genie3") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GENIE3" version)) (sha256 (base32 - "096crx7n75x60s9sx3l7nld3yvrsqs0clvjsdarxc6bbn2qxk81i")))) + "1q4wi3k95c8vsyfx6359p2p29ascjg1cxmpp9bf99ixbjs71rd33")))) (properties `((upstream-name . "GENIE3"))) (build-system r-build-system) (propagated-inputs @@ -15800,14 +16133,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.74.0") + (version "1.76.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "00pw6xmxjzprbx8wskq6gbyqkfak764vic5yxrzs6wpram352vmv")))) + "0fq59bwc5i8zdw0v0jr5j5lm4hk6p7b88i2xndsgj4fq65yr50g1")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (native-inputs @@ -15822,14 +16155,14 @@ Characteristic} (ROC) curves, with a focus on micro arrays.") (define-public r-watermelon (package (name "r-watermelon") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wateRmelon" version)) (sha256 (base32 - "0m8mra0jb6sgm13dagqn1pj81dha4dyj65xc6r2sh0yc3pyjb20h")))) + "0qslh2xhhyaf0nsgcqav6qgh05n8kp0s6p1zggc02iid30i1ibrj")))) (properties `((upstream-name . "wateRmelon"))) (build-system r-build-system) (propagated-inputs @@ -15860,14 +16193,14 @@ metrics, with methods for objects produced by the @code{methylumi} and (define-public r-gdsfmt (package (name "r-gdsfmt") - (version "1.34.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gdsfmt" version)) (sha256 (base32 - "1sx7yw44djrnc6km8fip3w3vclkgz5s0w6ibp8lpvmjcay8nv2sx")) + "10k445cwb5jhgcr0zf85x24mvldwk26zpwh0wq4himr44aha3bwx")) (modules '((guix build utils))) ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build ;; them and link with system libraries instead. @@ -15916,14 +16249,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-bigmelon (package (name "r-bigmelon") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigmelon" version)) (sha256 (base32 - "094d43yv8af8sijp43ndcaincnsf3ng32vgwh6bfazlq5d601r6y")))) + "1l1ym89qqbq6qx07bm2p8gcl5zd9xh0nbw10fb7s0pfbrkj8xy64")))) (properties `((upstream-name . "bigmelon"))) (build-system r-build-system) (propagated-inputs @@ -15935,8 +16268,7 @@ with multiple R processes supported by the package @code{parallel}.") r-methylumi r-minfi r-watermelon)) - (native-inputs - (list r-knitr)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/bigmelon/") (synopsis "Illumina methylation array analysis for large experiments") (description @@ -15947,14 +16279,14 @@ with multiple R processes supported by the package @code{parallel}.") (define-public r-seqbias (package (name "r-seqbias") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqbias" version)) (sha256 (base32 - "0mc6lv7vkch138n46gk1q1hfhv37mfxjij39q36wa0jy7s8cagfa")))) + "1sspl03m2hf6s5rw6nfqrycb236nvcgygql6apdlg3cjnikf090j")))) (properties `((upstream-name . "seqbias"))) (build-system r-build-system) (propagated-inputs @@ -15971,14 +16303,14 @@ genome sequence.") (define-public r-reqon (package (name "r-reqon") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReQON" version)) (sha256 (base32 - "1r4dzwnqv6a4zy5q9l3axqq23sbk9pjfb2y3fmwxjvdwq6c1qnp0")))) + "1knzla5d8n22121a9licrjh2rxrmh05304a9d4bs2f1r7aiwhgnh")))) (properties `((upstream-name . "ReQON"))) (build-system r-build-system) (propagated-inputs @@ -15994,14 +16326,14 @@ format.") (define-public r-wavcluster (package (name "r-wavcluster") - (version "2.32.0") + (version "2.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "wavClusteR" version)) (sha256 (base32 - "1z7y3wnrqr2xqrvs2xwmv419aqlizq0az17dpxmj1hg9knyls1bx")))) + "0491x3m0015g83m6a7pkc4783768clgykhlcmd2xr6cgrhih10g2")))) (properties `((upstream-name . "wavClusteR"))) (build-system r-build-system) (propagated-inputs @@ -16041,13 +16373,13 @@ procedures that induce nucleotide substitutions (e.g. BisSeq).") (define-public r-tilingarray (package (name "r-tilingarray") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tilingArray" version)) (sha256 (base32 - "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd")))) + "0wj3wb4x9s0v189p20rlwghsx82x314yyhhsnfmrl266qb1ambrn")))) (properties `((upstream-name . "tilingArray"))) (build-system r-build-system) (propagated-inputs @@ -16123,14 +16455,14 @@ provides methods for retrieving enriched pathways.") (define-public r-variantfiltering (package (name "r-variantfiltering") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantFiltering" version)) (sha256 (base32 - "110db9gcla796mbll3pin0hv2qp8r6khx0zzqfgzkp4mcyjxi62y")))) + "1j9fkqsxq7z3w2m435lqnrm8d17cd7l4873h26slmxhdazc9n94i")))) (properties `((upstream-name . "VariantFiltering"))) (build-system r-build-system) @@ -16229,14 +16561,14 @@ arrays based on fast wavelet-based functional models.") (define-public r-variancepartition (package (name "r-variancepartition") - (version "1.28.9") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "variancePartition" version)) (sha256 (base32 - "1al7wkbv26gldba61gq80c3mznsxwr7z5njv2s0lb7hnll9bscar")))) + "052xay39bzxyn0li631zy2nl08vp7q85q4phigwswpavfhl4w71g")))) (properties `((upstream-name . "variancePartition"))) (build-system r-build-system) @@ -16278,14 +16610,14 @@ measures.") (define-public r-htqpcr (package (name "r-htqpcr") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HTqPCR" version)) (sha256 (base32 - "1kclvh8f2sf534cjw07ry9nx74n6p7r0vmc3mk2nr37yvpf26b3q")))) + "12p0jb9bpz4x612vwj77d6l5h8rihfkzmhp8qy1gvv2zmn2a54jf")))) (properties `((upstream-name . "HTqPCR"))) (build-system r-build-system) (propagated-inputs @@ -16308,14 +16640,14 @@ features (e.g. genes, microRNAs).") (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "unifiedWMWqPCR" version)) (sha256 (base32 - "0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442")))) + "1gza678sd5m2rbki0l5hniki6gmds2cljkmywmk5v5m9swh9azq7")))) (properties `((upstream-name . "unifiedWMWqPCR"))) (build-system r-build-system) @@ -16332,14 +16664,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18")))) + "0v7c624y2sbqs6mc6kd6dynx24zakcilaswssxmplrcx15im87cn")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -16356,6 +16688,7 @@ data.") r-ggplot2 r-iranges r-mass + r-matrixgenerics r-rcpp r-rcppthread r-rlang @@ -16380,13 +16713,13 @@ motifs, and others.") (define-public r-ace (package (name "r-ace") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACE" version)) (sha256 (base32 - "12gmdkzm9wnrq793xqvw3mzwmmsm1vkh36llapr7m7q4dmcfgxr0")))) + "158v25ivbmsh54ywb5spfsd1nrmvfq83s8fkp14i7q5ckr2kvjhm")))) (properties `((upstream-name . "ACE"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-genomicranges r-ggplot2 r-qdnaseq)) @@ -16409,13 +16742,13 @@ of @dfn{tumor cells} (cells with divergent segments).") (define-public r-acgh (package (name "r-acgh") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aCGH" version)) (sha256 (base32 - "05q303bf8acvhbdzqxqk2gf12vg0fdqknlxryn2cs8nijx40zp46")))) + "0k8fbwhh1w0b0zy5qgixmcnwxi3v78f1bjmjg1yx6paniwk58bzn")))) (properties `((upstream-name . "aCGH"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-cluster r-multtest r-survival)) @@ -16433,13 +16766,13 @@ printing and plotting @code{aCGH} objects.") (define-public r-acme (package (name "r-acme") - (version "2.54.0") + (version "2.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ACME" version)) (sha256 (base32 - "0prcaxqmzm4hhpv228xh0glhm166gs17sa9h4lqrm03pwrjrdqdw")))) + "1z6j4wy355pljn9wf12zzq4zqrhaik0i2phy7jg89jsys7n2mlxy")))) (properties `((upstream-name . "ACME"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-biocgenerics)) @@ -16460,13 +16793,13 @@ on whole-genome tiling array experiments quite easily with enough memory.") (define-public r-acde (package (name "r-acde") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "acde" version)) (sha256 (base32 - "1d47hbna68qm517afk1wb0w9gb8j52p7nqh5axcc6h76zppsc1sp")))) + "088dq6mc9m1bx0dprcz8cdpfp447lnxq7420r139mhcik0z21vky")))) (properties `((upstream-name . "acde"))) (build-system r-build-system) (propagated-inputs (list r-boot)) @@ -16553,16 +16886,27 @@ cellular organization in health and disease.") (define-public r-bgmix (package (name "r-bgmix") - (version "1.58.0") + (version "1.59.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BGmix" version)) (sha256 (base32 - "0r4cxrjvf3qr5514lsw1s53h4by3djb9ipkz7bi979w343dn9xfx")))) + "16fzgxcy4sk0kd67vzdxqz81s84dvh4bqss9cbl9bn6vhpfsnfyf")))) (properties `((upstream-name . "BGmix"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; GCC's c++/bits/specfun.h (included by cmath) provides a std::beta + ;; procedure. + (add-after 'unpack 'avoid-naming-conflict + (lambda _ + (substitute* "src/BGmix_main.cpp" + (("\\bbeta\\b") "::beta") + (("\\*\\*::beta,") "**beta,"))))))) (propagated-inputs (list r-kernsmooth)) (home-page "https://bioconductor.org/packages/BGmix/") @@ -16575,14 +16919,14 @@ gene expression.") (define-public r-bgx (package (name "r-bgx") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bgx" version)) (sha256 (base32 - "1ylg9bnq8iwax0ap4c19v4mkbq673s8dfv49d94znsryg3fp93dl")))) + "1g6k3ryj8dz17asa4imnrk77z4dk9an5ssrqr17r0g797d5f4qjm")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) (arguments @@ -16611,14 +16955,14 @@ Affymetrix GeneChips.") (define-public r-bhc (package (name "r-bhc") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BHC" version)) (sha256 (base32 - "0ryd9lg8pywqlxj802y9jad5nxy40ivnzdq2ldldypwyalgk9ahm")))) + "0w60h1jr9kwvgg5d6bcrq4gl1aa1v6xrn43ymsc2312019psrrjy")))) (properties `((upstream-name . "BHC"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/BHC/") @@ -16637,18 +16981,18 @@ algorithm which is more efficient for larger data sets.") (define-public r-bicare (package (name "r-bicare") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BicARE" version)) (sha256 (base32 - "1z7x30705a4ww9vdam2668pk064na5ispigqnaqy8zqvlfvp3c8d")))) + "1q7dsvj6nvczs76jcxyy77298vgk4zk083bldmbbgnwparrgjii9")))) (properties `((upstream-name . "BicARE"))) (build-system r-build-system) (propagated-inputs - (list r-biobase r-gseabase r-multtest)) + (list r-biobase r-go-db r-gseabase r-multtest)) (home-page "http://bioinfo.curie.fr") (synopsis "Biclustering analysis and results exploration") (description @@ -16659,14 +17003,14 @@ results.") (define-public r-bifet (package (name "r-bifet") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiFET" version)) (sha256 (base32 - "0awzq3i7ga6jsh7xgmrpzz8klx69p8cxj73p6h7ya43bgcr0iff0")))) + "05lwz2pw2vnhmlhp5vv9j45jrc5ssdw4lx6mkxnsvds8zl3y9294")))) (properties `((upstream-name . "BiFET"))) (build-system r-build-system) (propagated-inputs @@ -16688,14 +17032,14 @@ the read count and GC content bias.") (define-public r-rsbml (package (name "r-rsbml") - (version "2.56.0") + (version "2.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rsbml" version)) (sha256 (base32 - "1syg49qz6vwzyw2zrxwrfb7kzgk0lim1q674f7mfvjah1fnv8bgc")))) + "0mgg1qfvxgyjk6fw4x0cv486vrsgf1kbqr6nqhgxj6lk8w6909fm")))) (properties `((upstream-name . "rsbml"))) (build-system r-build-system) (inputs @@ -16714,14 +17058,14 @@ validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") (define-public r-hypergraph (package (name "r-hypergraph") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hypergraph" version)) (sha256 (base32 - "1jvnvzjivjwqxh19c3g37kpyl6i6mxw99ma3ypjjgxzx898nsg45")))) + "13f3m8m6i99hzm94hriry645jcn0a1ki8z8wmn3mkasdi6bzx20h")))) (properties `((upstream-name . "hypergraph"))) (build-system r-build-system) (propagated-inputs @@ -16736,14 +17080,14 @@ manipulating hypergraphs.") (define-public r-hyperdraw (package (name "r-hyperdraw") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "hyperdraw" version)) (sha256 (base32 - "1fl4ia2jskvmbwk0y1wd0x4dgqph0av7bx2zffrvd1a5ppcjmsra")))) + "0vhfvmv6b3kab6a8hy2y9zwxgzwb5vliaaxhlrgz8i4pvvq5nhqb")))) (properties `((upstream-name . "hyperdraw"))) (build-system r-build-system) (inputs (list graphviz)) @@ -16758,14 +17102,14 @@ manipulating hypergraphs.") (define-public r-biggr (package (name "r-biggr") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiGGR" version)) (sha256 (base32 - "07b80qpkbas3x2yhndcm6vdkba0cpricyvnjf18dxklj5j612wfy")))) + "03pd4a3l912zdfk35flagikqimp01wp76nslid32l43d7yg9p57w")))) (properties `((upstream-name . "BiGGR"))) (build-system r-build-system) (propagated-inputs @@ -16822,14 +17166,14 @@ a file-backed matrix with factor properties.") (define-public r-bigpint (package (name "r-bigpint") - (version "1.14.0") + (version "1.15.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bigPint" version)) (sha256 (base32 - "1smf3w5a60jc0bpip5131ad9ykmnrcd33qi3pc3m50g6kn023wz2")))) + "1r9gr5f9as09ifagal5k7713h95qjw508cf8ny3j1jmqd24v6xhs")))) (properties `((upstream-name . "bigPint"))) (build-system r-build-system) (propagated-inputs @@ -16865,14 +17209,14 @@ visualizing RNA-sequencing datasets and differentially expressed genes.") (define-public r-chemminer (package (name "r-chemminer") - (version "3.50.0") + (version "3.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ChemmineR" version)) (sha256 (base32 - "0rk4ydanqxjh5yj0m9qlj06a12j7rkx9gxv6x7zpiyvnscahw63i")))) + "1m4vgq3z0kya7kbncawr9csvbwnh74mh012w7g2ialwd3nwdf91x")))) (properties `((upstream-name . "ChemmineR"))) (build-system r-build-system) (propagated-inputs @@ -16908,13 +17252,13 @@ structures.") (define-public r-fmcsr (package (name "r-fmcsr") - (version "1.40.0") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fmcsR" version)) (sha256 - (base32 "00xi01wz61ip8pnbrpnpp8hncb8gyiw69qkbg0cl425rv6qjb3mr")))) + (base32 "0ci77gbz93i3s2j2gjp7y3ssn6bcdcmqnl23smnjai7qjmln64dp")))) (properties `((upstream-name . "fmcsR"))) (build-system r-build-system) (propagated-inputs @@ -16937,14 +17281,14 @@ searching and clustering.") (define-public r-bioassayr (package (name "r-bioassayr") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioassayR" version)) (sha256 (base32 - "0r56r4qxibgblriyfbd46i8jhc2bfr9ndr8i30920v9kc3n83cav")))) + "0ilwniyrp3m8mi1vmggd17f9g6wdw7a78l2db190w29alzpbfmp6")))) (properties `((upstream-name . "bioassayR"))) (build-system r-build-system) (propagated-inputs @@ -16972,14 +17316,14 @@ available bioactivity data.") (define-public r-biobroom (package (name "r-biobroom") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobroom" version)) (sha256 (base32 - "02gdc26bs0yx7hb53b8ncipsaw6ynfvjcx64qxkxxq1c4awjkhzy")))) + "0kb6ylq94vywfky0mcrva109darcv361sqvwb19qn92p8vh5199l")))) (properties `((upstream-name . "biobroom"))) (build-system r-build-system) (propagated-inputs @@ -17001,18 +17345,19 @@ visualize bioinformatics analyses.") (define-public r-graphite (package (name "r-graphite") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graphite" version)) (sha256 (base32 - "0gkjab12ncag1vslc5bwlr0m5ac3ifq9ka5nfq7ckrpns98s7k0w")))) + "1fhjkgl6567qchi5sfdqnznalm1l7c7pabz8jc9d7ib9x4g922q5")))) (properties `((upstream-name . "graphite"))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi r-graph r-httr r-purrr r-rappdirs r-rlang)) + (native-inputs (list r-r-rsp)) (home-page "https://bioconductor.org/packages/graphite/") (synopsis "Networks from pathway databases") (description @@ -17024,14 +17369,14 @@ symbols).") (define-public r-reactomepa (package (name "r-reactomepa") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ReactomePA" version)) (sha256 (base32 - "06994hk9nrzlgz8sby61656rdbf1r954v71djl1i7141dgw5rif2")))) + "1hy8qz7d2826kf6pkl3v8cjwx35ap8xr92jw5wv445p3xcd1clzn")))) (properties `((upstream-name . "ReactomePA"))) (build-system r-build-system) (propagated-inputs @@ -17057,14 +17402,14 @@ enrichment analysis and several functions for visualization.") (define-public r-ebarrays (package (name "r-ebarrays") - (version "2.62.0") + (version "2.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EBarrays" version)) (sha256 (base32 - "0kg22appd9sd6knm129hchkamzilwr3h8wi4ibrvllbfmx31v9q8")))) + "1k50br4hpkrwv1lnn0wp1c7kj32vk0gg19aivmw5d6brjdd39c1f")))) (properties `((upstream-name . "EBarrays"))) (build-system r-build-system) (propagated-inputs @@ -17079,13 +17424,13 @@ microarray data.") (define-public r-biocbaseutils (package (name "r-biocbaseutils") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocBaseUtils" version)) (sha256 (base32 - "0p6siidrx8q6qr36fc67hzi091m2zwik3zngj27yllbfz6sn5k69")))) + "143fmjbi8spaj3njvc1xvsjszfxs7bv3vxik8pisw5y8lqzx7hqm")))) (properties `((upstream-name . "BiocBaseUtils"))) (build-system r-build-system) (native-inputs (list r-knitr)) @@ -17123,23 +17468,24 @@ monograph.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.34.3") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "00z2l5jnc028bmd3rl3qmgkd6k1mfa4p68kls34mkn29ic9ls22m")))) + "15f4jx4rkhi6aakdmy23dh3nlb2psaxkvwvrbya9vlsf5lmhajf9")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) (propagated-inputs - (list r-codetools + (list r-biocfilecache + r-biocmanager + r-biocviews + r-codetools r-graph r-httr r-knitr - r-biocmanager - r-biocviews r-stringdist)) (native-inputs (list r-knitr)) @@ -17152,14 +17498,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-biocgraph (package (name "r-biocgraph") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocGraph" version)) (sha256 (base32 - "0ysdmv2hyl8jnmr42lkyvgfqb0z89f5p649ahx0ygs6fw0z226xa")))) + "0fnncmi82qb9lkg1zfyps7n3nrw1s3wcqbixh420w53hmdyryryl")))) (properties `((upstream-name . "biocGraph"))) (build-system r-build-system) (propagated-inputs @@ -17174,13 +17520,13 @@ different graph related packages produced by Bioconductor.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.26.0") + (version "2.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "092hpmyhra755j32vc8w2l6xqwg09jm8apnk5rvxi1cm5034yvsl")))) + "04npnfmz1p1vpwrdsim309k7518i4p1li04xnmw8c9zgdb6yl61a")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -17198,13 +17544,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.66.3") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0ddxz7a8csf1l4srnjcgg5ps00fkcbv99y5wa0yrl6p9zr2d61qy")))) + "06gxyhxxnvcv6jxp5aqdsr35w1xhww2y5xafc3lw9wkawjdbnndy")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -17227,14 +17573,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.6.0") + (version "2.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s")))) + "0n55p4n2aadxh182lxxms3bk4bpajamivvqj06v09q2n9xnhjs7k")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -17242,7 +17588,6 @@ also known as views, in a controlled vocabulary.") r-biocfilecache r-biocgenerics r-biocmanager - r-curl r-rappdirs r-s4vectors)) (native-inputs @@ -17261,14 +17606,14 @@ access.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1as3k6avyc4l7saw02x0ql68c06msvs1s824vc1xg6lkdsi4lsyc")))) + "1zg30cb4s97zdv6c0f53ix6a97aan5w3lx698sa4cqvi4hbz8f35")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -17288,14 +17633,14 @@ access.") (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MultiAssayExperiment" version)) (sha256 (base32 - "00lhnqa4yz3lm5kl79bghad93iijihnassy2caf87czc540why09")))) + "00xgca1q9ai5x730bvx73f25lpwkr3dn2sia3msa49fpl4nrzr20")))) (properties `((upstream-name . "MultiAssayExperiment"))) (build-system r-build-system) @@ -17310,7 +17655,7 @@ access.") r-summarizedexperiment r-tidyr)) (native-inputs - (list r-knitr)) + (list r-knitr r-r-rsp)) (home-page "https://waldronlab.io/MultiAssayExperiment/") (synopsis "Integration of multi-omics experiments in Bioconductor") (description @@ -17325,14 +17670,14 @@ rownames.") (define-public r-bioconcotk (package (name "r-bioconcotk") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocOncoTK" version)) (sha256 (base32 - "1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s")))) + "11135a4l0vn84qmpyclz052zy45s0m38av94604jqxgb51q9lwyf")))) (properties `((upstream-name . "BiocOncoTK"))) (build-system r-build-system) (propagated-inputs @@ -17351,6 +17696,7 @@ rownames.") r-httr r-iranges r-magrittr + r-mass r-plyr r-rgraphviz r-rjson @@ -17370,14 +17716,14 @@ tools for genome-scale analysis of cancer studies.") (define-public r-biocor (package (name "r-biocor") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioCor" version)) (sha256 (base32 - "0a8xyrmarb2ja5zyvx5sndd67hylmwi29gpr5lwrzinww8w8b8w6")))) + "1aw8yh9l0jbjvkqgyzyr0wmwjh3ppmb0lwg8hxsfcv52ycsmvk7p")))) (properties `((upstream-name . "BioCor"))) (build-system r-build-system) (propagated-inputs @@ -17397,14 +17743,14 @@ gene selection, testing relationships, and so on.") (define-public r-biocpkgtools (package (name "r-biocpkgtools") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocPkgTools" version)) (sha256 (base32 - "0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf")) + "0s51dd9kjlh5vckwmynvahvg1pzl2ddvfn3s2kz77m0l0nbh7zfx")) (snippet '(for-each delete-file '("inst/htmlwidgets/lib/bioc_explore/bootstrap.min.js" @@ -17511,14 +17857,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0")))) + "1q5794gsinpy9hv5n1vx79bkqxi1jxzxjl95jlw9pqjmlnki07i5")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -17549,14 +17895,14 @@ accessing web references for elements/sets are also available in BiocSet.") (define-public r-biocworkflowtools (package (name "r-biocworkflowtools") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocWorkflowTools" version)) (sha256 (base32 - "00cy5lqmfap57bm2s00bis9ddci2lv1lrp0mk5ydgx061p4ym29i")))) + "1zvjj0hpqwdv7yifqwyb14166ppxw91d964gz4xclism5z5lvyln")))) (properties `((upstream-name . "BiocWorkflowTools"))) (build-system r-build-system) @@ -17582,14 +17928,14 @@ Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") (define-public r-biodist (package (name "r-biodist") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bioDist" version)) (sha256 (base32 - "1fnx3q5arsilrvnhndplap8h4ydi9bvmlpfllj1li124hn5n2w3d")))) + "1mx4abv7p76qsa0yzj0b4d03xklx09im01bx02lwa1w527gdmfc3")))) (properties `((upstream-name . "bioDist"))) (build-system r-build-system) (propagated-inputs @@ -17604,14 +17950,14 @@ distance measures.") (define-public r-pcatools (package (name "r-pcatools") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "PCAtools" version)) (sha256 (base32 - "1r32ajjmrhlwl0ylwavlfzph6m01mq3y7r87x8mbkmqw9ld1y2fd")))) + "07kl7s2zd7nkhg4hib2mr3w5lhqy780aw53yqsd7bfsjh53k8g95")))) (properties `((upstream-name . "PCAtools"))) (build-system r-build-system) (propagated-inputs @@ -17650,14 +17996,14 @@ dimensional mass cytometry data.") (define-public r-rgreat (package (name "r-rgreat") - (version "2.0.2") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rGREAT" version)) (sha256 (base32 - "1vmm7s5p8wqz1r8g1hy1l3mra3kkf76qgy5jkf84jxz7pi0clbld")))) + "0qq3fqzd973jlf6ibfww5yicnyz2qvs2b2mn35p77k2mp4d7qp52")))) (properties `((upstream-name . "rGREAT"))) (build-system r-build-system) (propagated-inputs @@ -17696,14 +18042,14 @@ user's input and automatically retrieving results from GREAT web server.") (define-public r-m3c (package (name "r-m3c") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "M3C" version)) (sha256 (base32 - "1djgbnxsdp1w9hhc6346gmvad3x8avy8nc85gpvg9i4x52wcrn4j")))) + "158brq3w5h735s9yq93xx0y4p79yhgz72rpy0cyk4fjia5yaij5c")))) (properties `((upstream-name . "M3C"))) (build-system r-build-system) (propagated-inputs @@ -17729,14 +18075,14 @@ hypothesis @code{K=1}.") (define-public r-icens (package (name "r-icens") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Icens" version)) (sha256 (base32 - "13ygc467nqh0235sf1ags1ihv7pg2yriva6qi7z46c534vxv6b8n")))) + "1aq4iwk1cp96jzldhx7d4q7i77zbdg8nzkzh12g29yhwzj39nl3q")))) (properties `((upstream-name . "Icens"))) (build-system r-build-system) (propagated-inputs @@ -17852,14 +18198,14 @@ generated.") (define-public r-preprocesscore (package (name "r-preprocesscore") - (version "1.60.2") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "preprocessCore" version)) (sha256 (base32 - "0ikxikmz9dy09g726q1wygymm6z2imlgfiizkgh1cl4s0m35fbbd")))) + "0z37ag22j1wh80vwq1kyr99rvadj9ppkddapfqyql3vj5x44cf4d")))) (properties `((upstream-name . "preprocessCore"))) (build-system r-build-system) @@ -17870,21 +18216,54 @@ generated.") routines.") (license license:lgpl2.0+))) +(define-public r-s4arrays + (package + (name "r-s4arrays") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "S4Arrays" version)) + (sha256 + (base32 + "05nbdz8c2qfkbflbn5acf4bvdb20rj83nb4aii0c5v4zvxxrs3js")))) + (properties `((upstream-name . "S4Arrays"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics r-crayon r-iranges r-matrix r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/S4Arrays") + (synopsis "Foundation of array-like containers in Bioconductor") + (description + "The S4Arrays package defines the @code{Array} virtual class to be +extended by other S4 classes that wish to implement a container with an +array-like semantic. It also provides: + +@enumerate +@item low-level functionality meant to help the developer of such container to + implement basic operations like display, subsetting, or coercion of their + array-like objects to an ordinary matrix or array, and +@item a framework that facilitates block processing of array-like + objects (typically on-disk objects). +@end enumerate +") + (license license:artistic2.0))) + (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.36.2") + (version "0.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "131cg5fzrqgyp4kv260yn8hpr0zv5mxjhdnpl50ydgc2k0l43d38")))) + "0qpjx64ilc1niglhf6pn47damgaf5vdzwkvnlhcixqzpl28ndbs9")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics)) + (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/S4Vectors") (synopsis "S4 implementation of vectors and lists") (description @@ -17940,14 +18319,14 @@ data manipulation and visualization.") (define-public r-rgraphviz (package (name "r-rgraphviz") - (version "2.42.0") + (version "2.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rgraphviz" version)) (sha256 (base32 - "0blymdax10zzg2lpj4hgvyh9c01b1qaivrc0gx95swji37zkqnwm")))) + "1dv1vk73achjz5b5zzw2d517nbjfrlj7gppd48pfhk1w0mvz3q61")))) (properties `((upstream-name . "Rgraphviz"))) (build-system r-build-system) (arguments @@ -17978,16 +18357,15 @@ objects from the @code{graph} package.") (define-public r-fishpond (package (name "r-fishpond") - (version "2.4.1") + (version "2.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fishpond" version)) (sha256 (base32 - "0kc1xzq03kz548rfinxhc7gxm6021502b6v7bg2har0aq4vx79ml")))) + "0lpafc1770kh4j151509d9lrpfj9jgla14km4vsfrqjmyhf2prss")))) (properties `((upstream-name . "fishpond"))) (build-system r-build-system) - (inputs (list zlib)) (propagated-inputs (list r-abind r-genomicranges @@ -18015,13 +18393,13 @@ working with Salmon and Alevin quantification files.") (define-public r-fithic (package (name "r-fithic") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1c7jscl82knbh5ha1i1hlm46nnhz6aw5h0j5xnl4hlgx8mnn05fl")))) + "0mqrzh1rcwyqlhq9wxcy4gp47hsb70qrsissm9nj0cb9j6ihi407")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -18039,13 +18417,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "10m3pq22a8m8bbfkmq5r44ydg2668g6dxmxp7km47jxgf9hlqhcl")))) + "00csfr3yhbllwc8797xg49qb0djpvbpfi6mbnps284nlqy5vpdwh")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -18068,14 +18446,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.26.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1y25mlsqf2inij6w2825xxl30bdba971az6rjf7j9bnya3gpvi6h")))) + "1riwxxnbi4z0lf42psh3m3ivxlgmmlnqhgsih6911c754r6s39qg")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -18088,6 +18466,7 @@ provided.") r-rhdf5 r-rhdf5filters r-rhdf5lib + r-s4arrays r-s4vectors)) (home-page "https://bioconductor.org/packages/HDF5Array") (synopsis "HDF5 back end for DelayedArray objects") @@ -18099,14 +18478,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0zxgpc2krfwqzm8c05cdlfs3dyyf5ll43ff9mw8xzj89wcmlcfx7")) + "1j8i4rmq85n7jys86a9zyj1n4qn7bhc1sqgcq8dyh7zqfdvb9bcw")) (modules '((guix build utils))) (snippet '(begin @@ -18179,14 +18558,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.14.2") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "1m7d227axnrlal1cy32z7i3hilzf55y0vlqg5xasv3m1n4kzihn4")))) + "0ga9y9npl885jdx7gw5h6lh7fr0z5p7cvcwpz3hvwm4dy235j6gj")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics r-delayedarray r-matrix r-rcpp)) @@ -18202,13 +18581,13 @@ matrices.") (define-public r-beadarraysnp (package (name "r-beadarraysnp") - (version "1.64.0") + (version "1.66.0") (source (origin (method url-fetch) (uri (bioconductor-uri "beadarraySNP" version)) (sha256 - (base32 "06hy89pclbyxjw5yf5i9bc3wr789b9pmhd9sdchgljlijs9vcj6g")))) + (base32 "1pymsm4j3wiyjvgsjb3vhjwdvhfmh91pxdhg4ihrj71pqpif3w9m")))) (properties `((upstream-name . "beadarraySNP"))) (build-system r-build-system) (propagated-inputs (list r-biobase r-quantsmooth)) @@ -18225,13 +18604,13 @@ performs copy number calculations and reports.") (define-public r-cner (package (name "r-cner") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CNEr" version)) (sha256 - (base32 "15y27ca14fdhn2prqgkyikff7p7490xn0bp2c7cnwhw173mm1syw")))) + (base32 "04arfcr2ay71hyy0xsh6jzappmcnnzfr1nyj1l7dqhhhk81ksjfd")))) (properties `((upstream-name . "CNEr"))) (build-system r-build-system) (inputs (list zlib)) @@ -18273,14 +18652,14 @@ advanced visualization of sets of conserved noncoding elements.") (define-public r-tfbstools (package (name "r-tfbstools") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "TFBSTools" version)) (sha256 (base32 - "05kgkwmh5mcrm0xd81rzicysgknb8wrf71y2llikvma1b9c1g789")))) + "136s96cmd1aq878xy9mqd4k46awywqpmm55lpvash8mv4gg02vg8")))) (properties `((upstream-name . "TFBSTools"))) (build-system r-build-system) (propagated-inputs @@ -18319,13 +18698,13 @@ provides a wrapper of de novo motif discovery software.") (define-public r-maftools (package (name "r-maftools") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "maftools" version)) (sha256 - (base32 "1f1r0frikaj6aw137dk523gagkxdygg7gzc3pd303ds5cqynwiqx")))) + (base32 "1jvmqn33hxzscr8j7y9zw5sngglcy0zkl0386053lx5dl5s5iqyq")))) (properties `((upstream-name . "maftools"))) (build-system r-build-system) (propagated-inputs @@ -18348,14 +18727,14 @@ customizable visualzations with minimal effort.") (define-public r-motifmatchr (package (name "r-motifmatchr") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifmatchr" version)) (sha256 (base32 - "01k2ngf4nj2cazb3a2c96by86xwdkdngzwhb73n2wadibamnqnfv")))) + "0vqsxfbrxs25xr27vsr5syqjn6fwvn5dw0g76w4rdqk5d08p56ci")))) (properties `((upstream-name . "motifmatchr"))) (build-system r-build-system) (propagated-inputs @@ -18382,13 +18761,13 @@ This package wraps C++ code from the MOODS motif calling library.") (define-public r-chromvar (package (name "r-chromvar") - (version "1.20.2") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "chromVAR" version)) (sha256 - (base32 "034in81lsdxa8j1na2zymck2y67235qprin8hak3dwa7lwzbm12z")))) + (base32 "001133rfcwmf4p3dbif933y9i1mkr3krw38g646wj4ikycszwih4")))) (properties `((upstream-name . "chromVAR"))) (build-system r-build-system) (propagated-inputs @@ -18429,14 +18808,14 @@ sequence (@code{DNAse-seq}) experiments.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.20.1") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1xwa6ncmqp21a4zx1dbs9p9b9rqbxhdgq2279mj4yl0gnpyqr9d7")))) + "1v2px6gvr0wzj2cyml57hxj5ghynlvizkchbywd3kx05j1h2mckd")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -18457,13 +18836,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6")))) + (base32 "0dwlg86wkivsag5ffjk81nlq34lwl3kk065k9l6lak24ziq6c4ij")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs @@ -18489,14 +18868,14 @@ cell types to infer the cell of origin of each single cell independently.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.8.4") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "04257gl995r575md1n3h2gy502yi6c8x3352l96mib7rdv4yg53f")))) + "13207k7b9qrpcngk4vd3jhc3zz815anwci1dqgadjyn4c8ragmnj")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -18524,13 +18903,13 @@ of other packages.") (define-public r-scater (package (name "r-scater") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1mjnf2y41lvni77g9hyw8qlvlsi5nxv5ha0fnch1kmw9814nycq3")))) + "0v6qaflv7b504yxxv6bmnlikg36bhfahgqxigpq6qcfrhqapmqck")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -18540,11 +18919,11 @@ of other packages.") r-biocsingular r-delayedarray r-delayedmatrixstats + r-densvis r-ggbeeswarm r-ggplot2 r-ggrepel r-ggrastr - r-gridextra r-matrix r-pheatmap r-rcolorbrewer @@ -18569,14 +18948,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.26.2") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0r80k4dsk609l9ha1jl64yhpwnf0x37i28k9largqsffsl6hw0fy")))) + "1qfmxarw5x17ag66r9i51vxm5h8fxm4rdicv6s8q5pnaf188hdcp")))) (build-system r-build-system) (propagated-inputs (list r-beachmat @@ -18612,14 +18991,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "1rq23ra4nnz9dx0gsg9bh8zcbz6s0pyvjwq30xl6g4hbqz927xb0")))) + "0yng347pnsrkbjgfw9xi20ms57kkbdgzh3sz3sj24dp6k0p5s3da")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -18637,14 +19016,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "0qcn7rlq0bsj11sc31wzks2xv900fpmbsblxp9cng5lj5cn2djk3")))) + "1mjdk76vmjzmmll0r73kfdi3x77hpdbk3jgzdqryxg4gna597q7j")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -18673,14 +19052,14 @@ memory usage and processing time is minimized.") (define-public r-mscoreutils (package (name "r-mscoreutils") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsCoreUtils" version)) (sha256 (base32 - "1shrvb2vmvk1m6xk59jqpvrxi8vzcr978aalbx1gjcmaqf6abzcq")))) + "055xzlq37d75ghfk87bxbsv4yifidnwxc3w2gp8mcqxwkxxhd70a")))) (properties `((upstream-name . "MsCoreUtils"))) (build-system r-build-system) (propagated-inputs @@ -18702,13 +19081,13 @@ within the R for Mass Spectrometry packages.") (define-public r-msfeatures (package (name "r-msfeatures") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MsFeatures" version)) (sha256 - (base32 "1q1224w31wdaagfv8ysc1w0d0n34y547c0jzkff1vxri9pb0w1j1")))) + (base32 "0cb4b0mf5yh8amqwa3r0mbk2f3rgq40gdlkhifk50fxnqdy4fjsh")))) (properties `((upstream-name . "MsFeatures"))) (build-system r-build-system) (propagated-inputs @@ -18732,14 +19111,14 @@ the respective packages (such as e.g. @code{xcms}).") (define-public r-biocio (package (name "r-biocio") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocIO" version)) (sha256 (base32 - "15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f")))) + "03hslg7k6khchf54gmlbkvwbkfn5ppz0wp7lh75gsnr0licsjkwx")))) (properties `((upstream-name . "BiocIO"))) (build-system r-build-system) (propagated-inputs @@ -18765,14 +19144,14 @@ as well as local access. Developers can register a file extension, e.g., (define-public r-msmseda (package (name "r-msmseda") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsEDA" version)) (sha256 (base32 - "17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v")))) + "108azzd6ibcgb1gqgcrz4shk3rdr3vfpzy0z6zknlsxwz7sbcnfi")))) (properties `((upstream-name . "msmsEDA"))) (build-system r-build-system) (propagated-inputs @@ -18788,14 +19167,14 @@ experiments, and visualize de influence of the involved factors.") (define-public r-msmstests (package (name "r-msmstests") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "msmsTests" version)) (sha256 (base32 - "10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3")))) + "1y3nklhlib2l9smcl6slv1653vyg9ip29if286l59rjrdwh50cwa")))) (properties `((upstream-name . "msmsTests"))) (build-system r-build-system) (propagated-inputs @@ -18817,14 +19196,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "0n3x5w074x5hhgdf2qa0pkma4vrjwrcgjna7hx0az6ixkgpbkrpv")))) + "0f6h0qngv7my83k402rydvi1pla695r5kxq02k1s5caxcsi1caza")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -18880,14 +19259,14 @@ preprocessing of cytometry data, including: (define-public r-erma (package (name "r-erma") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "06zxqzbzb0jrk357900gv1r2n81i49rbmrxla02f879kq2ik9cyd")))) + "14rgj8g9x248p2cc86aqn289qamsd91d6fnydi5d34q605ph73yj")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -18920,14 +19299,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1gm3y1nx0ah8wcrg2dh1xd688izm2sijz7bhgsasxckmmkmkp60g")))) + "0n7nghrrs7fp0b7jk2pfbkzl0lbv55xxk2xqnq2i77ps22ms0h9y")))) (build-system r-build-system) (arguments `(#:phases @@ -19088,14 +19467,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.42.1") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "01qs60sdh7c8cxkv3qbfcfwpjhab88j872va50fi95xsqnmj5isa")))) + "1lp345hxlddsc91lxrzay073g2dabc8h1cynyh87y85vzffhwplw")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -19137,14 +19516,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0sj51cli1p8k7z1nl5rfswjlzrk9cqnpr1a1pr618gk74kfwqf5a")))) + "1i64bk0ac2v0w5yjxdhnbjh05l6n9fi7gxap0zp73wxj7kl75wkd")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -19171,13 +19550,13 @@ EMBL-EBI GWAS catalog.") (define-public r-kegggraph (package (name "r-kegggraph") - (version "1.58.3") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGgraph" version)) (sha256 - (base32 "1s5j7zdp8ck4vhca81i4b6qclhwi56gmz8brawrxj3szvwmxf3y6")))) + (base32 "0bgigkmnz5zvsygcifk2fc7i8rahmqr4brk65qa3104clqqvdfkl")))) (properties `((upstream-name . "KEGGgraph"))) (build-system r-build-system) (propagated-inputs @@ -19195,26 +19574,20 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "0i8v4wfp207f5dpf3y2n8fqn7mc4khj92gb209vzc3y3kbwp2c6n")))) + "18gqmwwi1i4gndqljy809n5zzx38agawxxwhlknpas6k2iskd1xq")))) (build-system r-build-system) (propagated-inputs (list r-biocgenerics - r-ensdb-hsapiens-v75 - r-ensembldb - r-genomeinfodb - r-genomicfiles r-httr r-matrix - r-rsamtools - r-snpstats - r-variantannotation)) + r-rlang)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/ldblock") @@ -19319,13 +19692,13 @@ other functional sequencing data.") (define-public r-pathview (package (name "r-pathview") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pathview" version)) (sha256 - (base32 "0p7cdq03863zpw009prs1yh3gps1kw135anjfq6wpdkwza7xy4py")))) + (base32 "0mld7vys6s5k8snk1gniph9wkw3726vsx430nhyyr76fp4ps2mks")))) (properties `((upstream-name . "pathview"))) (build-system r-build-system) (propagated-inputs @@ -19353,13 +19726,13 @@ large-scale and fully automated analysis.") (define-public r-snapcgh (package (name "r-snapcgh") - (version "1.68.0") + (version "1.70.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snapCGH" version)) (sha256 (base32 - "1zxvl8mkby7yb5kppddag6k9w78d1fm6adx52h4cgrfckn28w64q")))) + "0yz5q7w3lqv8ac6a764xlbm4hq3ncnngqng879qbpmzhgb4r155g")))) (properties `((upstream-name . "snapCGH"))) (build-system r-build-system) (propagated-inputs @@ -19381,14 +19754,14 @@ segmented data for individual and multiple arrays.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "14rkrav4iydc85194skdy33sk365pjmmvxxvzaxxh0k9ds009qwx")))) + "1v2j2943apphs8i68ap9c8sxd4j5a04qda5scq4dqqkzqd0c5b6i")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs (list zlib)) @@ -19405,14 +19778,14 @@ the earlier snpMatrix package, allowing for uncertainty in genotypes.") (define-public r-chromstar (package (name "r-chromstar") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chromstaR" version)) (sha256 (base32 - "17p22vsmb9h8ap0f2rzyg2r71srj3sxiapzyaz1csad2vfjxfi2r")))) + "1qrcmydk080m1rzwbzx2km4vpbahnq5y73mrnpgjjjrxbndz9xz9")))) (properties `((upstream-name . "chromstaR"))) (build-system r-build-system) (propagated-inputs @@ -19443,14 +19816,14 @@ analyses.") (define-public r-guitar (package (name "r-guitar") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Guitar" version)) (sha256 (base32 - "0lrw1v82amr54bkfh98953b16fhlgd1i6kz1g7zy8gj0hd417ms1")))) + "1v1yw90waq0ccj6pxdipipy5bnk0k762m5kadl4h3jgpcrkf2fvc")))) (properties `((upstream-name . "Guitar"))) (build-system r-build-system) (propagated-inputs @@ -19496,14 +19869,14 @@ visualizations for publication-quality multi-panel figures.") (define-public r-ballgown (package (name "r-ballgown") - (version "2.30.0") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ballgown" version)) (sha256 (base32 - "0iy24vj4lg1k4fzdxf9blc47xsp4dmplajgabsb2s925l7jpxfvw")))) + "05lvpvy4gs3vg4ks23prx0mdp730h1m9kpg4al03ah062gyq3ahx")))) (properties `((upstream-name . "ballgown"))) (build-system r-build-system) (propagated-inputs @@ -19530,14 +19903,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.8.0") + (version "1.9.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "1krk5iqqzkkkxfgsvi9j6mj14i2rzisrrq0xmxjsrkgfh19awhr8")))) + "1sj4z63drafmm1hvs0yhhn9c9mrwiv8i2s0cjj1iam8rbar0xv79")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) @@ -19563,14 +19936,14 @@ regions or annotations of your choice from BigWig files.") (define-public r-beclear (package (name "r-beclear") - (version "2.14.0") + (version "2.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BEclear" version)) (sha256 (base32 - "05znaj2fialxi937mhj2dlrm3v4j2wgqafcy78qrkz7xxn13pr01")))) + "1sdw69dhrzkcpc7flvp1gkixvpsbrckyg756rlm17hjjwfxlz5lb")))) (properties `((upstream-name . "BEclear"))) (build-system r-build-system) (propagated-inputs @@ -19597,14 +19970,14 @@ real numbers.") (define-public r-bgeecall (package (name "r-bgeecall") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeCall" version)) (sha256 (base32 - "05w6b10vc4mmwdqnkcj7vnfigk03f03n776vqhlb38k0lx8k4hk3")))) + "0j83scxpq51bhxwfps7chcawzsqrd7pk7x2jg29zj4zbp1jbrnl0")))) (properties `((upstream-name . "BgeeCall"))) (build-system r-build-system) (propagated-inputs @@ -19633,14 +20006,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.24.0") + (version "2.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "14fja1dikzq60zjx1arcv1q16qd0hmibqjy0nbaivmk3zh16spkc")))) + "1s6v17bavidlfy6habi4bv6lmwkrx8c5was1zcq0kb05qdvpn4ph")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -19667,14 +20040,14 @@ anatomical terms, mapped to genes by expression patterns.") (define-public r-biobtreer (package (name "r-biobtreer") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biobtreeR" version)) (sha256 (base32 - "1j6w19k124x46gj2p8f1z0i2c03yhiiy1w0fqf504b2r7wy90jxc")))) + "0cbhlxh0w736695niyjd59fcvplna2f2x2av9k0sd1r3dy6lrcd4")))) (properties `((upstream-name . "biobtreeR"))) (build-system r-build-system) (propagated-inputs @@ -19691,14 +20064,14 @@ mappings functionalities.") (define-public r-minet (package (name "r-minet") - (version "3.56.0") + (version "3.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "minet" version)) (sha256 (base32 - "1xknyc2m03dyqrnx6np2y2lr41w06arl114f6cncl6wsnanqxzrz")))) + "04ll8nqhmyj2v12n2xskia8dh5px8mzj8fbyw1pzahk9vp085gkr")))) (properties `((upstream-name . "minet"))) (build-system r-build-system) (propagated-inputs @@ -19713,14 +20086,14 @@ information networks from data.") (define-public r-genetclassifier (package (name "r-genetclassifier") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geNetClassifier" version)) (sha256 (base32 - "1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2")))) + "1bn7h8jwmmgqzp0s3xdbsicm8pxmrgvnxmjnjs10d1rvp8znzjnn")))) (properties `((upstream-name . "geNetClassifier"))) (build-system r-build-system) @@ -19738,14 +20111,14 @@ interface to query the classifier.") (define-public r-dir-expiry (package (name "r-dir-expiry") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dir.expiry" version)) (sha256 (base32 - "1ix31jcfi3dg12pa0sz4k4izwc9rsydy6krl7f949lkam2g7s5f8")))) + "1vccq28734s7zk7pc7i9zq4rzbi373xqqvgkzamjpii36phkdmlw")))) (properties `((upstream-name . "dir.expiry"))) (build-system r-build-system) (propagated-inputs (list r-filelock)) @@ -19762,14 +20135,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0gh29w8arg0glawprwshaixv07y756c4lx21h8jjbqlsrbspp8fw")))) + "0qbff2mw0sj8i75vjs8f4qpsvsjgwncaz45a5bbzjgzbjw816xg4")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -19786,14 +20159,14 @@ package, primarily for creation of the underlying Conda instance.") (define-public r-basilisk (package (name "r-basilisk") - (version "1.10.2") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk" version)) (sha256 (base32 - "14sgm3ia7jj5jckysqkljrffafg6rl8i7fgzsxv8ycnrwbd05d09")))) + "02ai6ybxhj9q9mshkf17ivvqwsh9lhz7fig5wvr3m7a48hmqqg55")))) (properties `((upstream-name . "basilisk"))) (build-system r-build-system) (propagated-inputs @@ -19812,14 +20185,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.8.3") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "0h1cwir6m3zg728vdxxz03rfwysw92m9djdfj0vayixli2j4xz5a")))) + "1vzxr2wyv9vkkm4snn74w2l9nsiz3cim1s5gngzfw9wpli0a2kjf")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -19846,14 +20219,14 @@ Bioconductor-friendly.") (define-public r-biocdockermanager (package (name "r-biocdockermanager") - (version "1.10.0") + (version "1.11.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocDockerManager" version)) (sha256 (base32 - "13l5shmiiv4wl9m5xnwzagjxqrchjg9znvcgf7hv8f263l2yc8qm")))) + "0w393f14i253pnk0jzf2ci4g5cnxshwdjmix2r8arlnadh7spjyk")))) (properties `((upstream-name . "BiocDockerManager"))) (build-system r-build-system) @@ -19876,14 +20249,14 @@ the Bioconductor project.") (define-public r-biodb (package (name "r-biodb") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biodb" version)) (sha256 (base32 - "0mbqsias2ajw29d1wgl10y2cjqv3slrsgifccz0kh9l5r6bk28vz")))) + "1lcjq1zfarhc7pqqrkqnaycsv2f27n4n8mfvrc3c9ww4lsza555k")))) (properties `((upstream-name . "biodb"))) (build-system r-build-system) (propagated-inputs @@ -19921,14 +20294,14 @@ separate published packages.") (define-public r-biomformat (package (name "r-biomformat") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomformat" version)) (sha256 (base32 - "0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1")))) + "04kl2432wq6ybdhispvp98ylgyk3kkhmjx1nxdvcal7bfpy2vskk")))) (properties `((upstream-name . "biomformat"))) (build-system r-build-system) (propagated-inputs @@ -19950,14 +20323,14 @@ as extensions of common core functions/methods.") (define-public r-mvcclass (package (name "r-mvcclass") - (version "1.72.0") + (version "1.74.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MVCClass" version)) (sha256 (base32 - "1yzb7m7vk50f9x1g8yb95wlmpccj3n4qgczz46lvhsk7hkifybzq")))) + "1vrn2c5m4w7g13s1zd1am5b02lp026zg6gvpg8dvsras0j56rhr6")))) (properties `((upstream-name . "MVCClass"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/MVCClass") @@ -19970,14 +20343,14 @@ design.") (define-public r-biomvcclass (package (name "r-biomvcclass") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioMVCClass" version)) (sha256 (base32 - "1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk")))) + "07iay2dpq3margh1ny2snlc75g7fpfs5bf2gmhv88d31b8blg57r")))) (properties `((upstream-name . "BioMVCClass"))) (build-system r-build-system) (propagated-inputs @@ -20017,14 +20390,14 @@ using aCGH or sequencing.") (define-public r-bionero (package (name "r-bionero") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNERO" version)) (sha256 (base32 - "0ijdnl43cgzywgsz80jd6q0irixh6367qm1ll5ww1rcr4xas2nsl")))) + "0733v4mijf94gn0sbkhiinb3hxlsfqw2l89gx94k88sp3qy2qzvc")))) (properties `((upstream-name . "BioNERO"))) (build-system r-build-system) (propagated-inputs @@ -20073,14 +20446,14 @@ networks.") (define-public r-bionet (package (name "r-bionet") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNet" version)) (sha256 (base32 - "12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j")))) + "19caj3aj6gndkxkrd9s2x8v59hcdwdyxrx0ji473c3d5qrykskl1")))) (properties `((upstream-name . "BioNet"))) (build-system r-build-system) (propagated-inputs @@ -20102,16 +20475,29 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv")))) + "0bvfgppsdih6s70iizd7zh3zkb0hg4s4h1728xmyjqbvkl8fsdf4")) + (snippet + '(delete-file "inst/datatables/js/jquery.dataTables.min.js")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda _ + (with-directory-excursion "inst/datatables/js/" + (invoke "esbuild" + "jquery.dataTables.js" + "--minify" + "--outfile=jquery.dataTables.min.js"))))))) (propagated-inputs (list r-biocparallel r-dt @@ -20132,7 +20518,7 @@ scoring subnetwork.") r-whisker r-yaml)) (native-inputs - (list r-knitr)) + (list esbuild r-knitr r-rmarkdown)) (home-page "https://github.com/jardimViniciusC/BioNetStat") (synopsis "Biological network analysis") (description @@ -20144,14 +20530,14 @@ network and metabolic pathways view.") (define-public r-bioqc (package (name "r-bioqc") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioQC" version)) (sha256 (base32 - "1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf")))) + "0g6imi03l4xm0chx3i9wd2vdy0ls78lnylp294fq0jldl4n6y0nw")))) (properties `((upstream-name . "BioQC"))) (build-system r-build-system) (propagated-inputs @@ -20170,14 +20556,14 @@ optimised for high performance.") (define-public r-biotip (package (name "r-biotip") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BioTIP" version)) (sha256 (base32 - "1n90n4vz0cwz8irwpmrkm9qcyvk5rssl2v6wrzny4zwhzjkmvlni")))) + "0lqnxaycrva2092h4swmk6na2pq2kp951dmicyw399djd1i7yj50")))) (properties `((upstream-name . "BioTIP"))) (build-system r-build-system) (propagated-inputs @@ -20200,14 +20586,14 @@ help unravel disease regulatory trajectory.") (define-public r-biotmle (package (name "r-biotmle") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biotmle" version)) (sha256 (base32 - "1sbwbz0xdws31lsh46mfcijqmi6rm050r1d6vwii65q686x5j43w")))) + "1hjkhwbld8m52lsy2ba6cnp02n0xykaxm9650r5zmzry38dw9nb5")))) (properties `((upstream-name . "biotmle"))) (build-system r-build-system) (propagated-inputs @@ -20242,14 +20628,14 @@ ensemble machine learning for the estimation of nuisance functions.") (define-public r-bsseq (package (name "r-bsseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bsseq" version)) (sha256 (base32 - "0rd0ihr1ai1kvly2zf5y2qx3qyhk3ag2mdsrwqnzs67xkv99glsf")))) + "1mvhh99h1l6f5rlz0fzqkjpz9hblj2rbv8nx4j9n93g8riz7wsi3")))) (properties `((upstream-name . "bsseq"))) (build-system r-build-system) (propagated-inputs @@ -20288,13 +20674,13 @@ visualizing bisulfite sequencing data.") (define-public r-dada2 (package (name "r-dada2") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dada2" version)) (sha256 (base32 - "1cdfq4qa4kkfkqnkyxyr109hbvj5li396rm3p2b11qm2pxmfd7kc")))) + "1vxy2106rzygy0dr38wmw84zrqp9gsvaphliikdmhx0n2gv6xhd1")))) (properties `((upstream-name . "dada2"))) (build-system r-build-system) (propagated-inputs @@ -20325,14 +20711,14 @@ fragments by exact matching.") (define-public r-dmrseq (package (name "r-dmrseq") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "dmrseq" version)) (sha256 (base32 - "0djd2r0xzjcyw496wdw2gwzk4wjf3jp639b198x4pc0g0mmgw245")))) + "1xj23dqvmxi1sn4qn4zwvn9ggv128kr3gxmd7906463s9ap8qjja")))) (properties `((upstream-name . "dmrseq"))) (build-system r-build-system) (propagated-inputs @@ -20371,13 +20757,13 @@ interest on transformed methylation proportions.") (define-public r-omicade4 (package (name "r-omicade4") - (version "1.38.0") + (version "1.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "omicade4" version)) (sha256 (base32 - "1w9fsg0r6ir9nmmpf08b1mh8mnrzxk3f398y1w5dg34fdz4phgpg")))) + "086nh0m82gjlxyg6i230wpkin4zc3a7cfla0qzvj28h0n8irkm5r")))) (properties `((upstream-name . "omicade4"))) (build-system r-build-system) (propagated-inputs (list r-ade4 r-biobase r-made4)) @@ -20390,13 +20776,13 @@ interest on transformed methylation proportions.") (define-public r-omnipathr (package (name "r-omnipathr") - (version "3.5.25") + (version "3.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OmnipathR" version)) (sha256 - (base32 "1a0d4vf8i45h1fifswx9lhk6fk0z8sxfnav35psz9kvmxxab9698")))) + (base32 "0r2nv3nbadnvqby7p5bdpl9fxjb30h0c8kjv1dkqqnhk5rbfl4hf")))) (properties `((upstream-name . "OmnipathR"))) (build-system r-build-system) (arguments @@ -20445,14 +20831,14 @@ for ligand activity prediction from transcriptomics data.") (define-public r-biscuiteer (package (name "r-biscuiteer") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biscuiteer" version)) (sha256 (base32 - "1fq2nj0vclpxavqj5qx7jc3ympg00izxn9fpy4mlhyp9l921z13m")))) + "07nak6mfw9m8ldl336sqgkl3638ibv1hxwd89hwxdrn914wz3hw3")))) (properties `((upstream-name . "biscuiteer"))) (build-system r-build-system) (propagated-inputs @@ -20552,13 +20938,13 @@ starburst plots) in order to easily develop complete analysis pipelines.") (define-public r-tricycle (package (name "r-tricycle") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tricycle" version)) (sha256 (base32 - "0b5agqhywg23zxf0f9s1vfbzs7s7ijf9c716s7hwjprxfdz5znvw")))) + "1ags05rhi431jsk0kqs7rmxj853mf5c0ibfqknbwy2wmbz8p1vq6")))) (properties `((upstream-name . "tricycle"))) (build-system r-build-system) (propagated-inputs @@ -20591,14 +20977,14 @@ embeddings and functions to build new reference.") (define-public r-tximeta (package (name "r-tximeta") - (version "1.16.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximeta" version)) (sha256 (base32 - "15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa")))) + "03dmnpfffj18c6009qg985i596l4ckf3myin12g2p6xr56880bz1")))) (properties `((upstream-name . "tximeta"))) (build-system r-build-system) (propagated-inputs @@ -20632,13 +21018,13 @@ reproducibility.") (define-public r-phyloseq (package (name "r-phyloseq") - (version "1.42.0") + (version "1.44.0") (source (origin (method url-fetch) (uri (bioconductor-uri "phyloseq" version)) (sha256 - (base32 "07zi059v6zwrm31qwc7fmg35fwqlqfb6c30wwj9q4m2y67srnskk")))) + (base32 "0rmv8f1m8ck97v991wdly3fma2rjczhi974lh7ikwx6rcx6fp9ah")))) (properties `((upstream-name . "phyloseq"))) (build-system r-build-system) (propagated-inputs |