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path: root/gnu/packages/bioconductor.scm
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2023-12-15gnu: r-degreport: Update to 1.38.5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.38.5. [propagated-inputs]: Add r-dendextend and r-stringi. Change-Id: I73fe47489449b46406b879dba0318d02dc3c7614
2023-12-15gnu: r-cellid: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-cellid): Update to 1.10.1. Change-Id: I74f0e39907eb293f84a2ee9d29ef5feab15b698a
2023-12-15gnu: r-biocversion: Update to 3.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.18.1. Change-Id: I844d321dc3716d2658ddd75a81d844f8b302af53
2023-12-15gnu: r-bandits: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.18.1. Change-Id: Ied13d156cb7762fd6f86a5a0cccff302b684530d
2023-12-15gnu: r-aseb: Update to 1.46.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-aseb): Update to 1.46.3. Change-Id: I7fb905224840f598261fceba67207cd71e7a73d9
2023-12-15gnu: r-anvil: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.14.1. Change-Id: I2ea83e4a11a1268f222201480563fe1c9ce1060b
2023-12-15gnu: r-agimicrorna: Update to 2.52.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.52.0. Change-Id: I0f739590d115b5dc354833cdac2ba3c400ddd995
2023-12-15gnu: r-rhdf5lib: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.24.1. [propagated-inputs]: Add r-biocstyle and r-stringr. [native-inputs]: Add r-rmarkdown. Change-Id: I18c06543abee8e4a715f1ef120ce600562804225
2023-12-15gnu: r-reportingtools: Update to 2.42.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.42.3. [source]: Adjust snippet. [arguments]: Use minify-build-system in 'process-javascript phase. [native-inputs]: Remove r-knitr; add r-rmarkdown. Change-Id: I1c00e1a1d8095f40da29b57b8e82de493fcff26e
2023-12-15gnu: r-affycoretools: Update to 1.74.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.74.0. Change-Id: I4197d73e62477bb64182181229c8a33f3048406a
2023-12-15gnu: r-abn: Update to 3.0.4.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.4. Change-Id: I15970d14205b32f254ecf2c5207e98d7289ac281
2023-12-15gnu: r-fhtest: Update to 1.5.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-fhtest): Update to 1.5.1. Change-Id: I08513b08ee2fc72ab00b372a013dbfa6ed064fc1
2023-12-15gnu: r-biomartr: Update to 1.0.7.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.7. Change-Id: I7f02a92d86506b4fbca950a13ed106753e1b7f76
2023-12-15gnu: r-interactivedisplay: Add missing input.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-interactivedisplay)[propagated-inputs]: Add r-biocmanager. Change-Id: I7e29c28202496ba58ec35adf03b77ac84691e492
2023-12-15gnu: r-interactivedisplay: Add missing JavaScript sources.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-interactivedisplay)[source]: Update list of minified JavaScript files to delete. [arguments]: Use minify-build-system to process JavaScript files. [native-inputs]: Add js-d3-v2; relabel js-datatables as js-datatables-1.10; add js-datatables-1.9. Change-Id: If8b6d9378680e9f69d71be56ce28add70b1a4564
2023-12-15gnu: r-wgcna: Update to 1.72-5.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-wgcna): Update to 1.72-5. Change-Id: Ib9d3b0e6ba191839e4b22cb0b8f63e6b0e9d2baa
2023-12-11gnu: Add r-polyester.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-polyester): New variable. Change-Id: I415089cda3214ec04402fc6f4505fa868414d0e2 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-15gnu: r-abn: Update to 3.0.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.3. Change-Id: Id94ec47d805af9da63dbf43a9edbd5e7c3a5a62a
2023-11-15gnu: r-activepathways: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.3. Change-Id: I4199c307d48583c0894a39af78f6a4027cb0cf54
2023-11-15gnu: r-ggpicrust2: Update to 1.7.3.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.3. Change-Id: I18ab123d640ceec9315a21dff48ed2f1ea4ddff5
2023-11-13gnu: Add r-bcrank.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bcrank): New variable. Change-Id: Id43ae3b7f6eff54e1180b489c90fc72176751f9f
2023-11-13gnu: Add r-bbcanalyzer.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bbcanalyzer): New variable. Change-Id: Icd3c77c9522d73638ddb0934ad332ddb7b947a8e
2023-11-13gnu: Add r-baynorm.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-baynorm): New variable. Change-Id: I83e82d3d0362874918f423ab01f038c74f3eb265
2023-11-13gnu: Add r-bayesspace.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bayesspace): New variable. Change-Id: Id9c0d23e209bafea5941a1e1f968fab5f1724eab
2023-11-13gnu: Add r-bayesknockdown.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bayesknockdown): New variable. Change-Id: Icceffc04071efaa8a8b79144005fa7745abc7e1a
2023-11-13gnu: Add r-basicstarrseq.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-basicstarrseq): New variable. Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604
2023-11-13gnu: Add r-basics.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-basics): New variable. Change-Id: I6f0afeeb41f667d780707af65034d5ba978f0d4a
2023-11-13gnu: Add r-basic4cseq.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-basic4cseq): New variable. Change-Id: I8a031dc010590a8ef4655633026c9dfac35213c3
2023-11-13gnu: Add r-bsgenome-ecoli-ncbi-20080805.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bsgenome-ecoli-ncbi-20080805): New variable. Change-Id: Ic42527fa334be4c23ebe2e19461571d899db77ca
2023-11-13gnu: Add r-bags.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bags): New variable. Change-Id: If0c533898a5e05809f23e7e8b52fc3d5fbffc8fb
2023-11-13gnu: Add r-breastcancervdx.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-breastcancervdx): New variable. Change-Id: Ia3437ab67a00ce23c61553ff15f940b8a3ee9c8a
2023-11-04gnu: Add r-screpertoire.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-screpertoire): New variable. Change-Id: Iaa876f787d5e39ca2888bf2082da3d7839224e15
2023-11-04gnu: Add r-powertcr.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-powertcr): New variable. Change-Id: I75fc30a7021d6199b768318da3afcfeaaafcf027
2023-11-04gnu: Add r-rnbeads.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-rnbeads): New variable. Change-Id: I78b248a449473fc37ac414295faa6e61269b8625 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable. Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
2023-11-04gnu: Add r-methylaid.Mădălin Ionel Patrașcu
* gnu/packages/bioconductor.scm (r-methylaid): New variable. Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03gnu: Remove r-sigpathway.Ricardo Wurmus
This package has been removed with the release of Bioconductor 3.18. * gnu/packages/bioconductor.scm (r-sigpathway): Remove variable. Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
2023-11-03gnu: r-rhdf5filters: Simplify.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove 'use-system-libraries phase and pass configure flags to disable bundled libraries. Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
2023-11-03gnu: Remove r-genomegraphs.Ricardo Wurmus
This package had been removed from Bioconductor with release 3.11. * gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable. Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
2023-11-03gnu: Remove r-wavetiling.Ricardo Wurmus
This package had been removed from Bioconductor since release 3.12. * gnu/packages/bioconductor.scm (r-wavetiling): Remove variable. Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
2023-11-03gnu: r-mpo-db: Include HPO sqlite database.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-mpo-db)[arguments]: Bypass fetching of the database from the internet when in build environment. [native-inputs]: Add MPO.sqlite. Change-Id: Ic7228322b89ce78a85a9bd5ffbd985ccd906d268
2023-11-03gnu: r-hpo-db: Include HPO sqlite database.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-hpo-db)[arguments]: Bypass fetching of the database from the internet when in build environment. [native-inputs]: Add HPO.sqlite. Change-Id: Ie01605ef2531d992fb85c07bae5cfaabda626ea6
2023-11-03gnu: r-rhdf5lib: Adjust modifications to Makevars.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch. Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
2023-11-03gnu: r-phyloseq: Update to 1.46.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0. Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
2023-11-03gnu: r-tximeta: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0. Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
2023-11-03gnu: r-tricycle: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.10.0. Change-Id: I72a9e1140c17ce8605bfe6e83cc290eb1ae2fad2
2023-11-03gnu: r-tcgabiolinks: Update to 2.30.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.30.0. Change-Id: If7e571bfa6454bfa94dd395606575391dc506ecd
2023-11-03gnu: r-biscuiteer: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.16.0. Change-Id: Ib6cffbbeedfe87932acfcbfb2b789b4c92a9bf81
2023-11-03gnu: r-omnipathr: Update to 3.10.1.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omnipathr): Update to 3.10.1. [propagated-inputs]: Add r-lubridate and r-stringi. Change-Id: Ia18b66848cd6996dfdc551bf4b182bb5ac3e17a8
2023-11-03gnu: r-omicade4: Update to 1.42.0.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.42.0. Change-Id: I4369e5721116bf73f096ee39a516ada94c348872
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