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Author SHA1 Message Date
Ricardo Wurmus
73e20717d0
gnu: r-edger: Update to 4.0.3. 
* gnu/packages/bioconductor.scm (r-edger): Update to 4.0.3.

Change-Id: I97d73da131092effbf2404e710389d863ba39889
 2023-12-15 17:47:37 +01:00
Ricardo Wurmus
97d988cd23
gnu: r-champ: Update to 2.32.0. 
* gnu/packages/bioconductor.scm (r-champ): Update to 2.32.0.

Change-Id: I2058a0c0b086452ccfae5ef84884aa0b9cf51abb
 2023-12-15 17:47:37 +01:00
Ricardo Wurmus
b77fe732f0
gnu: r-annotationdbi: Update to 1.64.1. 
* gnu/packages/bioconductor.scm (r-annotationdbi): Update to 1.64.1.

Change-Id: If7f6bef70b3f4cc59c81ea68632b36c4b8449a73
 2023-12-15 17:47:37 +01:00
Ricardo Wurmus
96af9a059b
gnu: r-infercnv: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-infercnv): Update to 1.18.1.

Change-Id: I99b0f17246ef267a58f87c1719066b1b4f198d8b
 2023-12-15 17:47:37 +01:00
Ricardo Wurmus
da79581a8f
gnu: r-dmrcate: Update to 2.16.1. 
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 2.16.1.
[propagated-inputs]: Remove r-dss.

Change-Id: I183971826201b19cc88eb2768716aa2e165aba1f
 2023-12-15 17:47:36 +01:00
Ricardo Wurmus
ae4c47571e
gnu: r-degreport: Update to 1.38.5. 
* gnu/packages/bioconductor.scm (r-degreport): Update to 1.38.5.
[propagated-inputs]: Add r-dendextend and r-stringi.

Change-Id: I73fe47489449b46406b879dba0318d02dc3c7614
 2023-12-15 17:47:36 +01:00
Ricardo Wurmus
3dc5ddb82a
gnu: r-cellid: Update to 1.10.1. 
* gnu/packages/bioconductor.scm (r-cellid): Update to 1.10.1.

Change-Id: I74f0e39907eb293f84a2ee9d29ef5feab15b698a
 2023-12-15 17:47:36 +01:00
Ricardo Wurmus
f5f19ac400
gnu: r-biocversion: Update to 3.18.1. 
* gnu/packages/bioconductor.scm (r-biocversion): Update to 3.18.1.

Change-Id: I844d321dc3716d2658ddd75a81d844f8b302af53
 2023-12-15 17:47:35 +01:00
Ricardo Wurmus
71c0e7eea6
gnu: r-bandits: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-bandits): Update to 1.18.1.

Change-Id: Ied13d156cb7762fd6f86a5a0cccff302b684530d
 2023-12-15 17:47:35 +01:00
Ricardo Wurmus
ea9441de8f
gnu: r-aseb: Update to 1.46.3. 
* gnu/packages/bioconductor.scm (r-aseb): Update to 1.46.3.

Change-Id: I7fb905224840f598261fceba67207cd71e7a73d9
 2023-12-15 17:47:35 +01:00
Ricardo Wurmus
2dc2636444
gnu: r-anvil: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-anvil): Update to 1.14.1.

Change-Id: I2ea83e4a11a1268f222201480563fe1c9ce1060b
 2023-12-15 17:47:35 +01:00
Ricardo Wurmus
dafbf36e1f
gnu: r-agimicrorna: Update to 2.52.0. 
* gnu/packages/bioconductor.scm (r-agimicrorna): Update to 2.52.0.

Change-Id: I0f739590d115b5dc354833cdac2ba3c400ddd995
 2023-12-15 17:47:35 +01:00
Ricardo Wurmus
8341726732
gnu: r-rhdf5lib: Update to 1.24.1. 
* 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
 2023-12-15 17:27:44 +01:00
Ricardo Wurmus
c5f2535346
gnu: r-reportingtools: Update to 2.42.3. 
* 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
 2023-12-15 17:25:58 +01:00
Ricardo Wurmus
9013d47d5e
gnu: r-affycoretools: Update to 1.74.0. 
* gnu/packages/bioconductor.scm (r-affycoretools): Update to 1.74.0.

Change-Id: I4197d73e62477bb64182181229c8a33f3048406a
 2023-12-15 16:52:00 +01:00
Ricardo Wurmus
1354314cdf
gnu: r-abn: Update to 3.0.4. 
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.4.

Change-Id: I15970d14205b32f254ecf2c5207e98d7289ac281
 2023-12-15 16:13:07 +01:00
Ricardo Wurmus
b6c482e860
gnu: r-fhtest: Update to 1.5.1. 
* gnu/packages/bioconductor.scm (r-fhtest): Update to 1.5.1.

Change-Id: I08513b08ee2fc72ab00b372a013dbfa6ed064fc1
 2023-12-15 16:13:07 +01:00
Ricardo Wurmus
c544f5ce82
gnu: r-biomartr: Update to 1.0.7. 
* gnu/packages/bioconductor.scm (r-biomartr): Update to 1.0.7.

Change-Id: I7f02a92d86506b4fbca950a13ed106753e1b7f76
 2023-12-15 16:13:07 +01:00
Ricardo Wurmus
8f72116222
gnu: r-interactivedisplay: Add missing input. 
* gnu/packages/bioconductor.scm (r-interactivedisplay)[propagated-inputs]: Add
r-biocmanager.

Change-Id: I7e29c28202496ba58ec35adf03b77ac84691e492
 2023-12-15 16:13:07 +01:00
Ricardo Wurmus
2efa72be46
gnu: r-interactivedisplay: Add missing JavaScript sources. 
* 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
 2023-12-15 16:13:07 +01:00
Ricardo Wurmus
1da863cc3b
gnu: r-wgcna: Update to 1.72-5. 
* gnu/packages/bioconductor.scm (r-wgcna): Update to 1.72-5.

Change-Id: Ib9d3b0e6ba191839e4b22cb0b8f63e6b0e9d2baa
 2023-12-15 16:13:07 +01:00
Mădălin Ionel Patrașcu
9535cee6cd
gnu: Add r-polyester. 
* gnu/packages/bioconductor.scm (r-polyester): New variable.

Change-Id: I415089cda3214ec04402fc6f4505fa868414d0e2
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-12-11 06:27:42 +01:00
Ricardo Wurmus
9b270ccefa
gnu: r-abn: Update to 3.0.3. 
* gnu/packages/bioconductor.scm (r-abn): Update to 3.0.3.

Change-Id: Id94ec47d805af9da63dbf43a9edbd5e7c3a5a62a
 2023-11-15 15:55:20 +01:00
Ricardo Wurmus
fefc250c60
gnu: r-activepathways: Update to 2.0.3. 
* gnu/packages/bioconductor.scm (r-activepathways): Update to 2.0.3.

Change-Id: I4199c307d48583c0894a39af78f6a4027cb0cf54
 2023-11-15 15:55:20 +01:00
Ricardo Wurmus
285dd08443
gnu: r-ggpicrust2: Update to 1.7.3. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 1.7.3.

Change-Id: I18ab123d640ceec9315a21dff48ed2f1ea4ddff5
 2023-11-15 15:55:20 +01:00
Mădălin Ionel Patrașcu
a0d337e79c
gnu: Add r-bcrank. 
* gnu/packages/bioconductor.scm (r-bcrank): New variable.

Change-Id: Id43ae3b7f6eff54e1180b489c90fc72176751f9f
 2023-11-13 15:05:26 +01:00
Mădălin Ionel Patrașcu
08c745dcfc
gnu: Add r-bbcanalyzer. 
* gnu/packages/bioconductor.scm (r-bbcanalyzer): New variable.

Change-Id: Icd3c77c9522d73638ddb0934ad332ddb7b947a8e
 2023-11-13 15:05:26 +01:00
Mădălin Ionel Patrașcu
17978740e5
gnu: Add r-baynorm. 
* gnu/packages/bioconductor.scm (r-baynorm): New variable.

Change-Id: I83e82d3d0362874918f423ab01f038c74f3eb265
 2023-11-13 15:05:26 +01:00
Mădălin Ionel Patrașcu
53b4e01e29
gnu: Add r-bayesspace. 
* gnu/packages/bioconductor.scm (r-bayesspace): New variable.

Change-Id: Id9c0d23e209bafea5941a1e1f968fab5f1724eab
 2023-11-13 15:03:29 +01:00
Mădălin Ionel Patrașcu
598b911334
gnu: Add r-bayesknockdown. 
* gnu/packages/bioconductor.scm (r-bayesknockdown): New variable.

Change-Id: Icceffc04071efaa8a8b79144005fa7745abc7e1a
 2023-11-13 15:01:15 +01:00
Mădălin Ionel Patrașcu
77025bd511
gnu: Add r-basicstarrseq. 
* gnu/packages/bioconductor.scm (r-basicstarrseq): New variable.

Change-Id: I88f314877ea4ab98976820a4acc337ae3a34e604
 2023-11-13 15:00:48 +01:00
Mădălin Ionel Patrașcu
4e1c6f4998
gnu: Add r-basics. 
* gnu/packages/bioconductor.scm (r-basics): New variable.

Change-Id: I6f0afeeb41f667d780707af65034d5ba978f0d4a
 2023-11-13 15:00:00 +01:00
Mădălin Ionel Patrașcu
47a4195649
gnu: Add r-basic4cseq. 
* gnu/packages/bioconductor.scm (r-basic4cseq): New variable.

Change-Id: I8a031dc010590a8ef4655633026c9dfac35213c3
 2023-11-13 14:59:26 +01:00
Mădălin Ionel Patrașcu
459d9ebd2a
gnu: Add r-bsgenome-ecoli-ncbi-20080805. 
* gnu/packages/bioconductor.scm (r-bsgenome-ecoli-ncbi-20080805):
    New variable.

Change-Id: Ic42527fa334be4c23ebe2e19461571d899db77ca
 2023-11-13 14:57:00 +01:00
Mădălin Ionel Patrașcu
628926de80
gnu: Add r-bags. 
* gnu/packages/bioconductor.scm (r-bags): New variable.

Change-Id: If0c533898a5e05809f23e7e8b52fc3d5fbffc8fb
 2023-11-13 14:55:55 +01:00
Mădălin Ionel Patrașcu
d0251c23b9
gnu: Add r-breastcancervdx. 
* gnu/packages/bioconductor.scm (r-breastcancervdx): New variable.

Change-Id: Ia3437ab67a00ce23c61553ff15f940b8a3ee9c8a
 2023-11-13 14:55:55 +01:00
Mădălin Ionel Patrașcu
adf716c171
gnu: Add r-screpertoire. 
* gnu/packages/bioconductor.scm (r-screpertoire): New variable.

Change-Id: Iaa876f787d5e39ca2888bf2082da3d7839224e15
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
01b7d917a2
gnu: Add r-powertcr. 
* gnu/packages/bioconductor.scm (r-powertcr): New variable.

Change-Id: I75fc30a7021d6199b768318da3afcfeaaafcf027
 2023-11-04 23:13:51 +01:00
Mădălin Ionel Patrașcu
58786c82df
gnu: Add r-rnbeads. 
* gnu/packages/bioconductor.scm (r-rnbeads): New variable.

Change-Id: I78b248a449473fc37ac414295faa6e61269b8625
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 17:09:53 +01:00
Mădălin Ionel Patrașcu
cb0e60cccf
gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked. 
* gnu/packages/bioconductor.scm
  (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.

Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
 2023-11-04 16:30:11 +01:00
Mădălin Ionel Patrașcu
7eeab6417f
gnu: Add r-methylaid. 
* gnu/packages/bioconductor.scm (r-methylaid): New variable.

Change-Id: I7839035e5316bdbe5f1386b7b41ed2fc440fb432
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2023-11-04 11:37:15 +01:00
Ricardo Wurmus
8be2f44765
gnu: Remove r-sigpathway. 
This package has been removed with the release of Bioconductor 3.18.

* gnu/packages/bioconductor.scm (r-sigpathway): Remove variable.

Change-Id: I5cb9d938f370aa28b196f9cea95fb6024c2e6e37
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
38b5777ec8
gnu: r-rhdf5filters: Simplify. 
* gnu/packages/bioconductor.scm (r-rhdf5filters)[arguments]: Remove
'use-system-libraries phase and pass configure flags to disable bundled
libraries.

Change-Id: I2fb115e7b3df00cccb3f8d6659d465075d21f19b
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
142313cf0c
gnu: Remove r-genomegraphs. 
This package had been removed from Bioconductor with release 3.11.

* gnu/packages/bioconductor.scm (r-genomegraphs): Remove variable.

Change-Id: I73cc8cc8546089d91212176939b8c0c0a7afc309
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
0150529188
gnu: Remove r-wavetiling. 
This package had been removed from Bioconductor since release 3.12.

* gnu/packages/bioconductor.scm (r-wavetiling): Remove variable.

Change-Id: I5eb624d975f0eb170b263266b144eacf11944580
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
abaca151b2
gnu: r-mpo-db: Include HPO sqlite database. 
* 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
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
c66c66ee3f
gnu: r-hpo-db: Include HPO sqlite database. 
* 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
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
a938342899
gnu: r-rhdf5lib: Adjust modifications to Makevars. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Adjust patch.

Change-Id: Iaef3d2d80c22de1c2a0b64e7c13f5fa3b8e5719d
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
c82c9c8090
gnu: r-phyloseq: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.46.0.

Change-Id: Id11b5e913529ac8efce0d046168f4a9dbe0dbabd
 2023-11-03 22:49:28 +01:00
Ricardo Wurmus
1c3e8ab395
gnu: r-tximeta: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.20.0.

Change-Id: I8d9c5d01efc8f6c64290cdfdd193d95cd1da9152
 2023-11-03 22:49:28 +01:00