diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 155 |
1 files changed, 104 insertions, 51 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 265a70cdd4..ec52cd6e2d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2977,13 +2977,13 @@ for use in Bioconductor’s AnnotationHub.") (define-public r-anvil (package (name "r-anvil") - (version "1.12.0") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "AnVIL" version)) (sha256 (base32 - "17c5l10s756yzg69wdlwir88g0hn6zd0pdsycfr31n9n29nq59wa")))) + "0dx10gcch6csk8nw3ffz4yvn5jf0v80ynsp3dg1az0ybkqyrzbih")))) (properties `((upstream-name . "AnVIL"))) (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 "1.25.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "alpine" version)) (sha256 (base32 - "01y467qcjl40fq0m9vq6fpyi5f243v4g67dnn5ddqwrzrkyb0j2r")))) + "1md4m9ln1mpxf7d2h7jnsjyi4zrviiqn9fzk1gkz2n6qj7jwpqbb")))) (properties `((upstream-name . "alpine"))) (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 "3.2.2") + (version "3.2.3") (source (origin (method url-fetch) (uri (bioconductor-uri "bambu" version)) (sha256 (base32 - "0vmfynsyl1bdkbaxp278sgs52kmixi8kzzjck69arbnvmg0wp9ib")))) + "1b5zmyj75fjhyn4mb70gdqvxg76fg2z45vns9l0rl66s3p5mhm6d")))) (properties `((upstream-name . "bambu"))) (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 "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "dearseq" version)) (sha256 (base32 - "023kychm361z4zxyq9rmbx44p2nf7ysq2anlhn0q257v0bkwxn9i")))) + "12ld1f3892ag1a3lmkwjlkk6pd79ibykg8jrmddx2x33k23cv67g")))) (build-system r-build-system) (propagated-inputs (list r-compquadform @@ -4735,13 +4735,13 @@ bases such as COSMIC.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.26.2") + (version "0.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0zp49ksqcgy5bzlf63s8zc7flv2x66qkn02h49wmyj5ix20al0a7")))) + "0m603v0l74nawid61hvqbyb2662c1djqp436p87pk4f04fvws67j")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -4769,13 +4769,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-densvis (package (name "r-densvis") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "densvis" version)) (sha256 (base32 - "1291gp5wj9c47y291c1hqb12dj2zh6xrf0g38kllspqg9885cs54")))) + "0ypwnxi7ilczcvf5lwvyh6ck0jpvn1x90aggq66yqnn6yjy5md8s")))) (properties `((upstream-name . "densvis"))) (build-system r-build-system) (propagated-inputs (list r-assertthat r-basilisk r-irlba r-rcpp @@ -5895,13 +5895,13 @@ only one command.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.34.1") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "14ddzx7c5d4c599zwfx03bz3bqvxfc748znk929g3200brggqkqd")))) + "0j0yi0g0zri0liy9xm2j3k848smhib5mmkvwcw6281iwnpn7yypq")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -5932,7 +5932,7 @@ only one command.") (string-append m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) (propagated-inputs - (list r-bh r-cpp11 r-codetools r-futile-logger r-snow)) + (list r-bh r-codetools r-cpp11 r-futile-logger r-snow)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/BiocParallel") @@ -5946,13 +5946,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.68.0") + (version "2.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0gcx07d1qbrhkw30gfg39ln9jm71bya9f7si142lzs3p3bask8a2")))) + "13cnjbq2iykv83ycb4151d7yys21s3v15fc72v3s02m1i92lqyq4")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -6608,13 +6608,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "3.42.2") + (version "3.42.4") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1vss3n2m12vf6wcspfly394b8g3mfbwkkw8ihz8nqpc2iqs399rj")))) + "1lyn017jqgn6d987zrk0kp2p2nw3mxf8zjspk31pky532p9pkhs3")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7321,13 +7321,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.56.0") + (version "3.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "01q0rq2xwjsqj4phym4885iblpvfwvi5nphmnq8l3ybs0ixm2g9w")))) + "02c559an6hzk00bbvlrq1qljsnby4a53ng9jj6ff570mc6pabjn6")))) (build-system r-build-system) (home-page "https://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -8855,13 +8855,13 @@ method applicable to massive single-cell datasets (>10,000 cells).") (define-public r-scmap (package (name "r-scmap") - (version "1.22.1") + (version "1.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scmap" version)) (sha256 - (base32 "184dp319967ba9wx2g1v4rivwy3csr44s7in1jk91d5hwj28nk09")))) + (base32 "06i3r7zybwcgnak9ml2jaz7fy70zjqdh28v03ckaqhvck49kdqdm")))) (properties `((upstream-name . "scmap"))) (build-system r-build-system) (propagated-inputs @@ -9523,14 +9523,14 @@ of gene-level counts.") (define-public r-valr (package (name "r-valr") - (version "0.6.7") + (version "0.6.8") (source (origin (method url-fetch) (uri (cran-uri "valr" version)) (sha256 (base32 - "1s8bjbban2a3cqhwgykmhkv5b748nscamfbv67v4cppjbdvlhb5s")))) + "156sqh474synjvdm1j332ab75rqab0n81d674xbgs3rfxlr2ksgz")))) (build-system r-build-system) (propagated-inputs (list r-broom @@ -9779,13 +9779,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0gn134nvgf86gnf4d4fvrvjyy3pvk3rpdabzyi4rzrpjprycf4sb")))) + (base32 "1p89i2dfwcgrdchdnxrywp3jjjn5jjs5bisrx5kav26yh2pyx1wk")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -9989,13 +9989,13 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-apeglm (package (name "r-apeglm") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "apeglm" version)) (sha256 (base32 - "1k02w2jk0s65x1l2axi80fk60nxyx8jbgkax5pxwrsbv7l84n3bl")))) + "19r1mhpkn3xy6l188c14k9xgn25xqc718bwrlmnz63lak6mp4ws7")))) (properties `((upstream-name . "apeglm"))) (build-system r-build-system) (propagated-inputs @@ -10118,6 +10118,57 @@ package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.") (license license:gpl2))) +(define-public r-mbecs + (package + (name "r-mbecs") + (version "1.4.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MBECS" version)) + (sha256 + (base32 "0gfr3c5k7xjd342zfdksgh22mrk3ryr4cp89nar0mlpgzxg4l4vz")))) + (properties `((upstream-name . "MBECS"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'set-HOME + ;; Fontconfig needs a writable cache + (lambda _ (setenv "HOME" "/tmp")))))) + (propagated-inputs + (list r-cluster + r-dplyr + r-ggplot2 + r-gridextra + r-limma + r-lme4 + r-lmertest + r-magrittr + r-markdown + r-matrix + r-pheatmap + r-phyloseq + r-rmarkdown + r-ruv + r-sva + r-tibble + r-tidyr + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/rmolbrich/MBECS") + (synopsis + "Evaluation and correction of batch effects in microbiome data-sets") + (description + "The @acronym{MBECS, Microbiome Batch Effect Correction Suite} provides a +set of functions to evaluate and mitigate unwated noise due to processing in +batches. To that end it incorporates a host of batch correcting algorithms +(BECA) from various packages. In addition it offers a correction and reporting +pipeline that provides a preliminary look at the characteristics of a data-set +before and after correcting for batch effects.") + (license license:artistic2.0))) + (define-public r-mbkmeans (package (name "r-mbkmeans") @@ -10262,13 +10313,13 @@ fitting of some classes of graphical Markov models.") (define-public r-ggpicrust2 (package (name "r-ggpicrust2") - (version "1.6.3") + (version "1.6.5") (source (origin (method url-fetch) (uri (cran-uri "ggpicrust2" version)) (sha256 (base32 - "1rw8p1wjj3pmmccyqkl0smgnqz2s4f22hy4kyl91w8ck64xmplzs")))) + "02ais1y3z85vykxd9975gz33s80d1nhivly6a07y98dbmlzjyr6a")))) (properties `((upstream-name . "ggpicrust2"))) (build-system r-build-system) (propagated-inputs (list r-aldex2 @@ -11123,14 +11174,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "0vix0mmx4idnxj2qaslgqrrgh97fk6p3g9p7lnf3l0915gwks1p1")))) + "1jwjnwakinfqfx8ajbl58lqdhsq06a25phxy3vsprh1glj37smf7")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -15169,14 +15220,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.14.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1h1h0qrbd55p16d62v50nfan07vvnrbb9kjzpqfw0n8dc2xjwj1c")))) + "1dgbvhsd0rki1skwrb4acd3cfy7c9slsjq1s7r2469zbs3xf12xc")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -17588,13 +17639,13 @@ functionality.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.68.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "06gxyhxxnvcv6jxp5aqdsr35w1xhww2y5xafc3lw9wkawjdbnndy")))) + "04rzrwxd9n4l3agmbkx03hhcmy2fx049q5n4glld46mvx3vjvc48")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -17604,8 +17655,8 @@ functionality.") r-graph r-rbgl r-rcurl - r-xml - r-runit)) + r-runit + r-xml)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biocViews") (synopsis "Bioconductor package categorization helper") @@ -18263,13 +18314,13 @@ routines.") (define-public r-s4arrays (package (name "r-s4arrays") - (version "1.0.1") + (version "1.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Arrays" version)) (sha256 (base32 - "05nbdz8c2qfkbflbn5acf4bvdb20rj83nb4aii0c5v4zvxxrs3js")))) + "1pwkbp94r8vv43vgxcgqzbs1njhqlahfgsbf8rhr0ndy1bjyly2g")))) (properties `((upstream-name . "S4Arrays"))) (build-system r-build-system) (propagated-inputs @@ -19674,14 +19725,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "2.7-3") + (version "2.7-5") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "02qmp3ky671fkpjq1vcb083zzvfn5gkf69rhvdlvg7siy5wrjll3")))) + "0ibznjhy7vmh2myarvmxy06rvddbpbarbp201px62mig2pb9aq4y")))) (build-system r-build-system) (inputs (list gsl)) @@ -19695,6 +19746,8 @@ on the plot.") r-rcpparmadillo r-rgraphviz r-rjags)) + (native-inputs + (list r-r-rsp)) (home-page "https://r-bayesian-networks.org/") (synopsis "Modelling multivariate data with additive bayesian networks") (description @@ -19947,14 +20000,14 @@ to annotation.") (define-public r-megadepth (package (name "r-megadepth") - (version "1.9.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "megadepth" version)) (sha256 (base32 - "1sj4z63drafmm1hvs0yhhn9c9mrwiv8i2s0cjj1iam8rbar0xv79")))) + "1zzhgfnrr3r5ismbbj9jcqss8mr8ll6p4d3z026ya2khb0i7clc7")))) (properties `((upstream-name . "megadepth"))) (build-system r-build-system) (inputs (list megadepth)) @@ -20179,14 +20232,14 @@ eliminating obsolete caches generated by old versions of packages.") (define-public r-basilisk-utils (package (name "r-basilisk-utils") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "basilisk.utils" version)) (sha256 (base32 - "0qbff2mw0sj8i75vjs8f4qpsvsjgwncaz45a5bbzjgzbjw816xg4")))) + "0g5apvna9wzjlm7g9hdafy44nrg5rp3qh4anwpgwwp2vr0vxn37k")))) (properties `((upstream-name . "basilisk.utils"))) (build-system r-build-system) @@ -20229,14 +20282,14 @@ Python environments in a single R session.") (define-public r-biocthis (package (name "r-biocthis") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biocthis" version)) (sha256 (base32 - "1vzxr2wyv9vkkm4snn74w2l9nsiz3cim1s5gngzfw9wpli0a2kjf")))) + "1kmgahjyyrvs475as24yk0jniswjaa507q6zs8zq8jjqa26gy6zj")))) (properties `((upstream-name . "biocthis"))) (build-system r-build-system) (arguments @@ -20927,13 +20980,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.25.3") + (version "2.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0daq7093yipry8pp6fj6pj8x1njxs8j6cz7875qkfmzqkbis4vql")))) + (base32 "16hpljnqskgv7mycj0ipfxhvkyy0hcqvnrn5m416plwcx5cj2fjm")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs |