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1597 Commits (34137c21458c72c3b96c6c27d013d94479741427)

Author SHA1 Message Date
Ricardo Wurmus 53ec97713a
gnu: Add r-metapod. 
* gnu/packages/bioconductor.scm (r-metapod): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus 8caab75883
gnu: Add r-ggtree. 
* gnu/packages/bioconductor.scm (r-ggtree): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus ab4a91b252
gnu: Add r-treeio. 
* gnu/packages/bioconductor.scm (r-treeio): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus fd4fa40ac4
gnu: Add r-scaledmatrix. 
* gnu/packages/bioconductor.scm (r-scaledmatrix): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus efefb2be3a
gnu: Add r-trajectoryutils. 
* gnu/packages/bioconductor.scm (r-trajectoryutils): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus ce99b4da63
gnu: Add r-restfulr. 
* gnu/packages/bioconductor.scm (r-restfulr): New variable.
 2021-06-05 09:12:39 +02:00
Ricardo Wurmus 8cc146b24a
gnu: r-bisquerna: Update to 1.0.5. 
* gnu/packages/bioconductor.scm (r-bisquerna): Update to 1.0.5.
[native-inputs]: Add r-knitr.
 2021-06-02 17:27:07 +02:00
Ricardo Wurmus ec543ba672
gnu: r-chipseeker: Move out of experiment section. 
* gnu/packages/bioconductor.scm (r-chipseeker): Move the package from the
"experiment" section to the section for regular Bioconductor packages.
 2021-05-31 15:54:41 +02:00
Ricardo Wurmus a6e7afd4d5
gnu: r-spp: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
 2021-05-31 15:53:20 +02:00
Ricardo Wurmus 1a6108ce2b
gnu: r-geneoverlap: Move out of experiment section. 
* gnu/packages/bioconductor.scm (r-geneoverlap): Move the package definition
out of the "experiment" section into the section for regular Bioconductor
packages.
 2021-05-31 15:53:09 +02:00
zimoun c294c0d782
gnu: r-methylkit: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
 2021-05-31 15:39:49 +02:00
zimoun 7ab44aeed6
gnu: r-copywriter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
 2021-05-31 15:39:49 +02:00
zimoun 36cb01066c
gnu: r-copyhelper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:39:47 +02:00
zimoun 31e50e1f48
gnu: r-chipseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 0eaa75c811
gnu: r-rhdf5: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun cc1dbea883
gnu: r-annotationfilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 67e99369c1
gnu: r-rhdf5filters: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun b6e84d30eb
gnu: r-tximport: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun bf8f502956
gnu: r-mutationalpatterns: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 7360dea624
gnu: r-rcas: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
 2021-05-31 15:39:00 +02:00
zimoun 45b6db4fb4
gnu: r-bamsignals: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
 2021-05-31 15:38:59 +02:00
zimoun 043c309d15
gnu: r-rhtslib: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
 2021-05-31 15:38:59 +02:00
zimoun e0c81584ea
gnu: r-zlibbioc: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
 2021-05-31 15:38:58 +02:00
zimoun 0006a66415
gnu: r-seqlogo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
 2021-05-31 15:38:21 +02:00
zimoun c2a18aee16
gnu: r-motifrg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 621aa3b442
gnu: r-sva: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 900ef8fb1e
gnu: r-protgenerics: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 720d2694a5
gnu: r-mzr: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
 2021-05-31 15:38:00 +02:00
zimoun 88cf24febb
gnu: r-ensembldb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun fea33b9d1e
gnu: r-biovizbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 8d4311bb8e
gnu: r-vsn: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 96ae9822c4
gnu: r-affyio: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 8182e6a6fd
gnu: r-organismdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun d1ea2b7c8b
gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 0b5b41c561
gnu: r-genomicfiles: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun ff65fa90d2
gnu: r-complexheatmap: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun 84019edf38
gnu: r-gage: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
 2021-05-31 15:37:59 +02:00
zimoun d0a5503752
gnu: r-keggrest: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 22cda2e432
gnu: r-affy: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 32ae36e96f
gnu: r-fastseg: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 9644745692
gnu: r-annotationhub: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun dfe6224f5f
gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun f6f43a2d40
gnu: r-edaseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun ef954bb488
gnu: r-deseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun bb118f20fe
gnu: r-aroma-light: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun 7756e08b44
gnu: r-mzid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
 2021-05-31 15:37:58 +02:00
zimoun ad46c8aa7f
gnu: r-pcamethods: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
 2021-05-31 15:37:57 +02:00
zimoun d7fa9c1ffd
gnu: r-genomationdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
 2021-05-31 15:37:55 +02:00
zimoun f8fe5497c7
gnu: r-genomation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
 2021-05-31 15:36:32 +02:00
zimoun f3b50aa4fd
gnu: r-go-db: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
 2021-05-31 15:35:53 +02:00
zimoun 14fb30e5f6
gnu: r-seqpattern: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
 2021-05-31 15:35:30 +02:00
zimoun b832fddbfc
gnu: r-impute: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
 2021-05-31 15:34:45 +02:00
zimoun a2a1d86a77
gnu: r-samr: Move to (gnu packages bioconductor). 
* gnu/packages/cran.scm (r-samr): Move from here...
* gnu/packages/bioconductor.scm (r-samr): ...to here.
 2021-05-31 15:34:45 +02:00
zimoun 4f030cc0db
gnu: r-msnbase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 8c7c78bfce
gnu: r-msnid: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 537d48d869
gnu: r-bsgenome: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun 90bbab5cff
gnu: r-topgo: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun f78ff75b41
gnu: r-genomicfeatures: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun a88230a1bc
gnu: r-rtracklayer: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
 2021-05-31 15:34:44 +02:00
zimoun ca1a015777
gnu: r-genomicalignments: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
 2021-05-31 15:34:39 +02:00
Roel Janssen cf9ddbd4bc
gnu: Add r-tradeseq. 
* gnu/packages/bioconductor.scm (r-tradeseq): New variable.
 2021-05-27 13:40:10 +02:00
Roel Janssen 5abf8a56ee
gnu: Add r-slingshot. 
* gnu/packages/bioconductor.scm (r-slingshot): New variable.
 2021-05-27 13:31:29 +02:00
Roel Janssen 2fc74f3176
gnu: Add r-clusterexperiment. 
* gnu/packages/bioconductor.scm (r-clusterexperiment): New variable.
 2021-05-26 23:54:14 +02:00
Roel Janssen 700b10f181
gnu: Add r-mbkmeans. 
* gnu/packages/bioconductor.scm (r-mbkmeans): New variable.
 2021-05-26 23:49:28 +02:00
Roel Janssen 1edec0e899
gnu: Add r-zinbwave. 
* gnu/packages/bioconductor.scm (r-zinbwave): New variable.
 2021-05-26 23:09:06 +02:00
Roel Janssen 4e9bb49688
gnu: Add r-structuralvariantannotation. 
* gnu/packages/bioconductor.scm (r-structuralvariantannotation): New variable.
 2021-05-26 16:07:17 +02:00
Roel Janssen f921981536
gnu: Add r-decipher. 
* gnu/packages/bioconductor.scm (r-decipher): New variable.
 2021-05-26 13:31:20 +02:00
Roel Janssen 99873359ed
gnu: Add r-deepsnv. 
* gnu/packages/bioconductor.scm (r-deepsnv): New variable.
 2021-05-26 13:13:56 +02:00
Roel Janssen 834f649590
gnu: Add r-geneoverlap. 
* gnu/packages/bioconductor.scm (r-geneoverlap): New variable.
 2021-05-26 13:09:34 +02:00
Roel Janssen 94b8ad4490
gnu: Add r-chipseeker. 
* gnu/packages/bioconductor.scm (r-chipseeker): New variable.
 2021-05-26 10:21:32 +02:00
Roel Janssen 9048e7f3b4
gnu: Add r-bsgenome-btaurus-ucsc-bostau8. 
* gnu/packages/bioconductor.scm (r-bsgenome-btaurus-ucsc-bostau8): New
  variable.
 2021-05-26 09:42:01 +02:00
Roel Janssen b84ead8c04
gnu: Add r-aneufinder. 
* gnu/packages/bioconductor.scm (r-aneufinder): New variable.
 2021-05-26 09:13:54 +02:00
Roel Janssen 189311660b
gnu: Add r-aneufinderdata. 
* gnu/packages/bioconductor.scm (r-aneufinderdata): New variable.
 2021-05-26 09:13:08 +02:00
Ricardo Wurmus 1d7470874e
gnu: r-multidataset: Update to 1.18.2. 
* gnu/packages/bioconductor.scm (r-multidataset): Update to 1.18.2.
 2021-05-20 14:43:34 +02:00
Ricardo Wurmus bee797fa93
gnu: Add r-guitar. 
* gnu/packages/bioconductor.scm (r-guitar): New variable.
 2021-05-04 15:37:04 +02:00
Ricardo Wurmus 7694acebd1
gnu: r-summarizedexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here...
* gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here.
 2021-05-04 10:11:34 +02:00
Ricardo Wurmus b602ec9fba
gnu: r-mixomics: Update to 6.14.1. 
* gnu/packages/bioconductor.scm (r-mixomics): Update to 6.14.1.
[propagated-inputs]: Add r-biocparallel.
 2021-05-04 09:47:37 +02:00
Ricardo Wurmus 4286233e77
gnu: r-catalyst: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-catalyst): Update to 1.14.1.
 2021-05-04 09:47:37 +02:00
Ricardo Wurmus 2191a414ea
gnu: r-scran: Update to 1.18.7. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.18.7.
 2021-05-04 09:47:37 +02:00
Ricardo Wurmus 3c59d34107
gnu: r-biocpkgtools: Update to 1.8.2. 
* gnu/packages/bioconductor.scm (r-biocpkgtools): Update to 1.8.2.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus b75b3ba2c7
gnu: r-experimenthub: Update to 1.16.1. 
* gnu/packages/bioconductor.scm (r-experimenthub): Update to 1.16.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus c1942727cf
gnu: r-bioassayr: Update to 1.28.3. 
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.3.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 5bd5f755f2
gnu: r-universalmotif: Update to 1.8.5. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.8.5.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus b410f072b5
gnu: r-icobra: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-icobra): Update to 1.18.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus b2bdc2f130
gnu: r-interactionset: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 390098ddd4
gnu: r-systempiper: Update to 1.24.6. 
* gnu/packages/bioconductor.scm (r-systempiper): Update to 1.24.6.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus fc1aef2ccd
gnu: r-genomeinfodb: Update to 1.26.7. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.7.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus 8bd3170bcf
gnu: r-biocgenerics: Update to 0.36.1. 
* gnu/packages/bioconductor.scm (r-biocgenerics): Update to 0.36.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus aa9a94bba9
gnu: r-abn: Update to 2.5-0. 
* gnu/packages/cran.scm (r-abn): Move from here...
* gnu/packages/bioconductor.scm (r-abn): ...to here; update to 2.5-0.
[propagated-inputs]: Add r-rgraphviz.
 2021-05-04 07:27:43 +02:00
Vagrant Cascadian eb34afe1be
gnu: r-circrnaprofiler: Fix grammar. 
* gnu/packages/bioconductor.scm (r-circrnaprofiler)[description]:
  Remove gratuitous use of "allows to".
 2021-04-21 08:34:21 -07:00
Vagrant Cascadian 0e434dad70
gnu: r-msmstests: Fix typo. 
* gnu/packages/bioconductor.scm (r-msmstests)[description]: Fix "This
  package" typo.
 2021-04-21 08:30:47 -07:00
hli eb8da54170
gnu: Add r-txdb-dmelanogaster-ucsc-dm6-ensgene. 
* gnu/packages/bioconductor.scm (r-txdb-dmelanogaster-ucsc-dm6-ensgene):
New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-04-12 18:25:40 +02:00
Tobias Geerinckx-Rice 48358a25ca
gnu: r-gagedata: Fix typo in synopsis. 
* gnu/packages/bioconductor.scm (r-gagedata)[synopsis]: Fix typo and add
article.
 2021-04-10 14:11:34 +02:00
Tobias Geerinckx-Rice 04a5e7918d
gnu: r-chromstar: Fix typo in description. 
* gnu/packages/bioconductor.scm (r-chromstar)[description]: Fix typo.
 2021-04-10 14:11:32 +02:00
Tobias Geerinckx-Rice 37d4706166
gnu: r-msmstests: Fix typos in description. 
* gnu/packages/bioconductor.scm (r-msmstests)[description]: Fix typos.
 2021-04-10 14:11:29 +02:00
Ricardo Wurmus e0147aa46f
gnu: r-gviz: Update to 1.34.1. 
* gnu/packages/bioconductor.scm (r-gviz): Update to 1.34.1.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus 14a4c30828
gnu: r-universalmotif: Update to 1.8.4. 
* gnu/packages/bioconductor.scm (r-universalmotif): Update to 1.8.4.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus 8a7933f37e
gnu: r-rsubread: Update to 2.4.3. 
* gnu/packages/bioconductor.scm (r-rsubread): Update to 2.4.3.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus 215b0ced02
gnu: r-chippeakanno: Update to 3.24.2. 
* gnu/packages/bioconductor.scm (r-chippeakanno): Update to 3.24.2.
[propagated-inputs]: Add r-dplyr.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus 55185f9b3f
gnu: r-diffbind: Update to 3.0.15. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.15.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus 9d2ca98213
gnu: r-genomeinfodb: Update to 1.26.6. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.6.
 2021-04-08 13:28:24 +02:00
Ricardo Wurmus fb73d7d10d
gnu: r-delayedarray: Update to 0.16.3. 
* gnu/packages/bioconductor.scm (r-delayedarray): Update to 0.16.3.
 2021-04-08 13:28:23 +02:00
zimoun 23686ba3eb
Revert "Revert some commits that caused `guix pull` to fail." 
This reverts commit 8ec0ca8faf.
 2021-03-31 21:23:45 +02:00
zimoun 9282218508
gnu: r-absfiltergsea: Move to (gnu packages bioconductor). 
* gnu/packages/cran.scm (r-absfiltergsea): Move this variable from here...
* gnu/packages/bioconductor.scm (r-absfiltergsea): ...to here.
 2021-03-31 21:23:45 +02:00
zimoun 172b85aa99
gnu: r-bisquerna: Move to (gnu packages bioconductor). 
* gnu/packages/cran.scm (r-bisquerna): Move this variable from here...
* gnu/packages/bioconductor.scm (r-bisquerna): ...to here.
 2021-03-31 21:23:45 +02:00
Hong Li 0ff888108a
gnu: Add r-chromstar. 
* gnu/packages/bioconductor.scm (r-chromstar): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-03-22 14:27:13 +01:00
Hong Li 1f958631ef
gnu: Add r-chromstardata. 
* gnu/packages/bioconductor.scm (r-chromstardata): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-03-22 14:26:58 +01:00
Leo Famulari 8ec0ca8faf
Revert some commits that caused `guix pull` to fail. 
This reverts commits 821e643921 through
8f9fd9b70c.

Specifically, these commits caused the build failure of
guix-package-cache.drv like this:

------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
 2021-03-15 19:52:34 -04:00
Ricardo Wurmus 8f9fd9b70c
gnu: r-biocparallel: Build reproducibly. 
* gnu/packages/bioconductor.scm (r-biocparallel)[arguments]: Add phase
"make-reproducible".
 2021-03-15 23:31:58 +01:00
zimoun d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun adf45daae9
gnu: r-rsamtools: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun 821e643921
gnu: r-limma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
 2021-03-15 23:30:26 +01:00
Ricardo Wurmus 1ada8ea96c
gnu: r-scater: Update to 1.18.6. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.6.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus fa6bb614c8
gnu: r-cytoml: Update to 2.2.2. 
* gnu/packages/bioconductor.scm (r-cytoml): Update to 2.2.2.
[inputs]: Add zlib.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus 11dc49afc2
gnu: r-diffbind: Update to 3.0.14. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.14.
 2021-03-15 15:03:07 +01:00
Ricardo Wurmus ee61edb621
gnu: r-reportingtools: Update to 2.30.2. 
* gnu/packages/bioconductor.scm (r-reportingtools): Update to 2.30.2.
 2021-03-15 15:03:07 +01:00
Ricardo Wurmus fa227c9640
gnu: r-genomeinfodb: Update to 1.26.4. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.26.4.
 2021-03-15 15:03:07 +01:00
Ricardo Wurmus b45c625f10
gnu: r-deseq2: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.30.1.
 2021-03-15 15:03:07 +01:00
zimoun bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
 2021-03-15 14:06:24 +01:00
zimoun 082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
 2021-03-15 14:06:16 +01:00
zimoun 35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
 2021-03-15 14:05:56 +01:00
zimoun 8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
 2021-03-15 14:05:47 +01:00
zimoun 9949f459bf
gnu: r-iranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
 2021-03-15 14:05:37 +01:00
zimoun d64e3a487b
gnu: r-s4vectors: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
 2021-03-15 14:05:27 +01:00
zimoun 852fa82d4c
gnu: r-bioccheck: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
 2021-03-15 14:05:22 +01:00
zimoun d5576b6eb7
gnu: r-grohmm: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
 2021-03-15 14:04:26 +01:00
zimoun 5ac55aea8b
gnu: r-biocstyle: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
 2021-03-15 14:03:21 +01:00
zimoun 134404b437
gnu: r-biocviews: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
 2021-03-15 14:03:18 +01:00
Ricardo Wurmus 3eeb7dbf04
gnu: r-gkmsvm: Move back to (gnu packages cran). 
* gnu/packages/bioconductor.scm (r-gkmsvm): Move this variable from here...
* gnu/packages/cran.scm (r-gkmsvm): ...to here.
 2021-03-15 12:15:18 +01:00
zimoun df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
 2021-03-12 14:45:55 +01:00
zimoun 8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun 031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun 373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
 2021-03-12 14:45:53 +01:00
Ricardo Wurmus 323aec6ad9
gnu: r-bioassayr: Update home page. 
* gnu/packages/bioconductor.scm (r-bioassayr)[home-page]: Follow permanent
redirect.
 2021-03-12 14:41:15 +01:00
zimoun 2528cad451
gnu: r-bioassayr: Update to 1.28.2. 
* gnu/packages/bioconductor.scm (r-bioassayr): Update to 1.28.2.
 2021-03-12 14:41:14 +01:00
zimoun 8c8d365ca3
gnu: r-chemminer: Update to 3.42.2. 
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.2.
 2021-03-12 14:41:14 +01:00
zimoun 4f617bfb8e
gnu: r-circrnaprofiler: Update to 1.4.2. 
* gnu/packages/bioconductor.scm (r-circrnaprofiler): Update to 1.4.2.
 2021-03-12 14:41:14 +01:00
Ricardo Wurmus ef8e4f4172
gnu: r-wgcna: Update to 1.70-3. 
* gnu/packages/bioconductor.scm (r-wgcna): Update to 1.70-3.
 2021-03-09 22:05:24 +01:00
Mădălin Ionel Patrașcu 297531ef58
gnu: Add r-circrnaprofiler. 
* gnu/packages/bioconductor.scm (r-circrnaprofiler): New variable.
 2021-03-05 16:07:06 +01:00
Mădălin Ionel Patrașcu 1353e53605
gnu: Add r-universalmotif. 
* gnu/packages/bioconductor.scm (r-universalmotif): New variable.
 2021-03-05 16:07:06 +01:00
Ricardo Wurmus 89d7c8efc6
gnu: Add r-chromvar. 
* gnu/packages/bioconductor.scm (r-chromvar): New variable.
 2021-02-18 15:57:52 +01:00
Ricardo Wurmus 9a38f39ec0
gnu: Add r-motifmatchr. 
* gnu/packages/bioconductor.scm (r-motifmatchr): New variable.
 2021-02-18 15:40:44 +01:00
Ricardo Wurmus 2def2e203f
gnu: Add r-tfbstools. 
* gnu/packages/bioconductor.scm (r-tfbstools): New variable.
 2021-02-18 15:35:38 +01:00
Ricardo Wurmus e6bc150b0c
gnu: Add r-cner. 
* gnu/packages/bioconductor.scm (r-cner): New variable.
 2021-02-18 15:19:46 +01:00
Ricardo Wurmus 311bb4bc3d
gnu: r-delayedmatrixstats: Update to 1.12.3. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.3.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus 8acfd9f3d4
gnu: r-sparsematrixstats: Update to 1.2.1. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): Update to 1.2.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus de4fc49270
gnu: r-scran: Update to 1.18.5. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.18.5.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus cf3e703820
gnu: r-scuttle: Update to 1.0.4. 
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.0.4.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus 79d51ffeca
gnu: r-beachmat: Update to 2.6.4. 
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.4.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus a1357422c3
gnu: r-rhdf5lib: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.12.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus f7947f8991
gnu: r-hdf5array: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.18.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus 18ebacaa1c
gnu: r-preprocesscore: Update to 1.52.1. 
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.52.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus da109ae738
gnu: r-chemminer: Update to 3.42.1. 
* gnu/packages/bioconductor.scm (r-chemminer): Update to 3.42.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus 6f37c3ea40
gnu: r-gdsfmt: Update to 1.26.1. 
* gnu/packages/bioconductor.scm (r-gdsfmt): Update to 1.26.1.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus 9470f901d9
gnu: r-cytolib: Update to 2.2.1. 
* gnu/packages/bioconductor.scm (r-cytolib): Update to 2.2.1.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus 691178d67b
gnu: r-multidataset: Update to 1.18.1. 
* gnu/packages/bioconductor.scm (r-multidataset): Update to 1.18.1.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus 6d0709231f
gnu: r-clusterprofiler: Update to 3.18.1. 
* gnu/packages/bioconductor.scm (r-clusterprofiler): Update to 3.18.1.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus ebf9ad7984
gnu: r-enrichplot: Update to 1.10.2. 
* gnu/packages/bioconductor.scm (r-enrichplot): Update to 1.10.2.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus 669ea5ab09
gnu: r-matrixgenerics: Update to 1.2.1. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): Update to 1.2.1.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus 61609fb88e
gnu: r-diffbind: Update to 3.0.13. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.13.
 2021-02-11 21:33:36 +01:00
Ricardo Wurmus a7d6e1b6a1
gnu: r-ldheatmap: Move to (gnu packages bioconductor). 
This is a follow-up to commit 0c8bb20b7c.

* gnu/packages/cran.scm (r-ldheatmap): Move this from here...
* gnu/packages/bioconductor.scm (r-ldheatmap): ...to here.
 2020-12-29 22:17:37 +01:00
zimoun 610cd6a170
gnu: r-ggbio: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 81f481d6cd
gnu: r-gqtlstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 61ec8928c7
gnu: r-snpstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun a2c66d18a5
gnu: r-homo-sapiens: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
 2020-12-29 17:40:28 +01:00
zimoun 8c2b7c9a2a
gnu: r-erma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 8f1237c350
gnu: r-ldblock: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 9534e7b706
gnu: r-gqtlstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 2a4322f7c3
gnu: r-gviz: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 69a5e066c1
gnu: r-gwascat: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun 838db0de5e
gnu: r-sushi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
 2020-12-29 17:40:25 +01:00
Ricardo Wurmus 17235ec28c
gnu: r-nmf: Move from "annotation" to "package" section. 
* gnu/packages/bioconductor.scm (r-nmf): Move variable.
 2020-12-17 11:41:15 +01:00
Ricardo Wurmus eb3c105126
gnu: r-deconstructsigs: Move from "annotation" to "package" section. 
* gnu/packages/bioconductor.scm (r-deconstructsigs): Move variable.
 2020-12-17 11:40:31 +01:00
Ricardo Wurmus e7fa79fd91
gnu: r-pasilla: Move from "annotation" to "experiment" section. 
* gnu/packages/bioconductor.scm (r-pasilla): Move variable.
 2020-12-17 11:39:51 +01:00
Ricardo Wurmus cc54848ad0
gnu: r-ideoviz: Move from "annotation" to "package" section. 
* gnu/packages/bioconductor.scm (r-ideoviz): Move variable.
 2020-12-17 11:39:06 +01:00
Ricardo Wurmus e5610fd9f4
gnu: r-genelendatabase: Move from "annotation" to "experiment" section. 
* gnu/packages/bioconductor.scm (r-genelendatabase): Move variable.
 2020-12-17 11:38:24 +01:00
Ricardo Wurmus 30a4bd3bb3
gnu: r-bluster: Move from "annotation" to "package" section. 
* gnu/packages/bioconductor.scm (r-bluster): Move variable.
 2020-12-17 11:37:47 +01:00
Ricardo Wurmus 1abb6a2a78
gnu: r-cummerbund: Move from "experiment" to "package" section. 
* gnu/packages/bioconductor.scm (r-cummerbund): Move variable.
 2020-12-17 11:37:17 +01:00
Ricardo Wurmus 17d95689b4
gnu: r-coverageview: Move from "experiment" to "package" section. 
* gnu/packages/bioconductor.scm (r-coverageview): Move variable.
 2020-12-17 11:36:26 +01:00
Mădălin Ionel Patrașcu 04a0594662
gnu: Add r-org-eck12-eg-db. 
* gnu/packages/bioconductor.scm (r-org-eck12-eg-db): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-12-17 11:26:53 +01:00
Mădălin Ionel Patrașcu e4b0794e52
gnu: Add r-pathview. 
* gnu/packages/bioconductor.scm (r-pathview): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-12-17 11:26:53 +01:00
Mădălin Ionel Patrașcu 7395458d40
gnu: Add r-kegggraph. 
* gnu/packages/bioconductor.scm (r-kegggraph): New variable.
 2020-12-17 11:26:53 +01:00
Mădălin Ionel Patrașcu eb2f1a7dd9
gnu: Add r-gagedata. 
* gnu/packages/bioconductor.scm (r-gagedata): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2020-12-17 11:26:53 +01:00
Ricardo Wurmus 3872153a2f
gnu: r-scuttle: Update to 1.0.3. 
* gnu/packages/bioconductor.scm (r-scuttle): Update to 1.0.3.
[propagated-inputs]: Add r-genomicranges.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus eed728951c
gnu: r-beachmat: Update to 2.6.2. 
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.2.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus 589ac42212
gnu: r-cicero: Update to 1.8.1. 
* gnu/packages/bioconductor.scm (r-cicero): Update to 1.8.1.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus 7cda2d415f
gnu: r-biosigner: Update to 1.18.2. 
* gnu/packages/bioconductor.scm (r-biosigner): Update to 1.18.2.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus 4714787793
gnu: r-biocneighbors: Update to 1.8.2. 
* gnu/packages/bioconductor.scm (r-biocneighbors): Update to 1.8.2.
[propagated-inputs]: Remove r-rcppannoy.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus ebf11de4e3
gnu: r-diffbind: Update to 3.0.8. 
* gnu/packages/bioconductor.scm (r-diffbind): Update to 3.0.8.
 2020-12-09 12:12:48 +01:00
Ricardo Wurmus 4617cc7fd5
gnu: r-rhtslib: Propagate zlib. 
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
(r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
r-methylkit)[inputs]: Remove zlib.
* gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
 2020-12-09 12:12:48 +01:00
Ricardo Wurmus 7601015fc9
gnu: r-delayedmatrixstats: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.1.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:48 +01:00
zimoun 64f9fb308f
gnu: r-bigmelon: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-bigmelon): Update to 1.16.0.
 2020-12-09 12:12:48 +01:00
zimoun 9f6e2bfe1f
gnu: r-watermelon: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-watermelon): Update to 1.34.0.
 2020-12-09 12:12:47 +01:00
zimoun 8db36c1f68
gnu: r-yarn: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-yarn): Update to 1.16.0.
 2020-12-09 12:12:47 +01:00
zimoun adf6edc750
gnu: r-quantro: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-quantro): Update to 1.24.0.
 2020-12-09 12:12:47 +01:00
zimoun 4eeaa159d2
gnu: r-lumi: Update to 2.42.0. 
* gnu/packages/bioconductor.scm (r-lumi): Update to 2.42.0.
 2020-12-09 12:12:47 +01:00
zimoun 0b7dd44706
gnu: r-methylumi: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-methylumi): Update to 2.36.0.
 2020-12-09 12:12:47 +01:00
zimoun e5a4198bc3
gnu: r-minfi: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-minfi): Update to 1.36.0.
 2020-12-09 12:12:47 +01:00
zimoun 45dfb75166
gnu: Add r-catalyst. 
* gnu/packages/bioconductor.scm (r-catalyst): New variable.
 2020-12-09 12:12:47 +01:00
zimoun 43bf50ecae
gnu: r-ggcyto: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-ggcyto): Update to 1.18.0.
 2020-12-09 12:12:47 +01:00
zimoun b856a48768
gnu: r-scdd: Update to 1.14.0. 
* gnu/packages/bioconductor.scm (r-scdd): Update to 1.14.0.
 2020-12-09 12:12:47 +01:00
zimoun 3f04b8167b
gnu: r-chipcomp: Update to 1.20.0. 
* gnu/packages/bioconductor.scm (r-chipcomp): Update to 1.20.0.
 2020-12-09 12:12:47 +01:00
zimoun 1174317e03
gnu: r-pcatools: Update to 2.2.0. 
* gnu/packages/bioconductor.scm (r-pcatools): Update to 2.2.0.
 2020-12-09 12:12:47 +01:00
zimoun b03c955c6f
gnu: r-scran: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-scran): Update to 1.18.0.
[propagated-inputs]: Add r-bluster, r-scuttle.  Remove r-iranges.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:47 +01:00
zimoun d4b5d18684
gnu: r-scater: Update to 1.18.3. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.18.3.
[propagated-inputs]: Add r-gridextra, r-scutlle.  Remove r-beachmat, r-rcpp.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus 0e60dda0ae
gnu: Add r-scuttle. 
* gnu/packages/bioconductor.scm (r-scuttle): New variable.
 2020-12-09 12:12:46 +01:00
zimoun 10c87ecf77
gnu: r-delayedmatrixstats: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): Update to 1.12.0.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
 2020-12-09 12:12:46 +01:00
zimoun 4ef898d449
gnu: r-singlecellexperiment: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-singlecellexperiment): Update to 1.12.0.
 2020-12-09 12:12:46 +01:00
zimoun d0db04fcaf
gnu: r-yapsa: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-yapsa): Update to 1.16.0.
 2020-12-09 12:12:46 +01:00
zimoun 798ec28916
gnu: r-biocsingular: Update to 1.6.0. 
* gnu/packages/bioconductor.scm (r-biocsingular): Update to 1.6.0.
 2020-12-09 12:12:46 +01:00
zimoun dd9341ffa3
gnu: r-genomicinteractions: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-genomicinteractions): Update to 1.24.0.
 2020-12-09 12:12:46 +01:00
zimoun 35dae95110
gnu: r-interactionset: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-interactionset): Update to 1.18.0.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus 5e719988f2
gnu: Add r-sparsematrixstats. 
* gnu/packages/bioconductor.scm (r-sparsematrixstats): New variable.
 2020-12-09 12:12:46 +01:00
Roel Janssen a23310ffc2
gnu: Add r-bluster. 
* gnu/packages/bioconductor.scm (r-bluster): New variable.
 2020-12-09 12:12:45 +01:00
Roel Janssen aca4ebe40a
gnu: r-annaffy: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-annaffy): Update to 1.62.0.
 2020-12-09 12:12:45 +01:00
zimoun 16f16b5e21
gnu: Add r-msmstests. 
* gnu/packages/bioconductor.scm (r-msmstests): New variable.
 2020-12-09 12:12:43 +01:00
zimoun e520c68fa9
gnu: Add r-msmseda. 
* gnu/packages/bioconductor.scm (r-msmseq): New variable.
 2020-12-09 12:12:43 +01:00
Roel Janssen fe4ce29a5c
gnu: r-beachmat: Update to 2.6.1. 
* gnu/packages/bioconductor.scm (r-beachmat): Update to 2.6.1.
 2020-12-09 12:12:36 +01:00
zimoun 0022e9f4c0
gnu: r-ncdfflow: Fix r-rhdf5libs link. 
* gnu/packages/bioconductor.scm (r-ncdfflow): [arguments]: Avoid to have a
plain directory on the list of libraries to link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:36 +01:00
zimoun 2b224f904a
gnu: r-cytoml: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-cytoml): [arguments]: Avoid to have
a plain directory on the list of libraries to link.
 2020-12-09 12:12:36 +01:00
zimoun ece564f07d
gnu: r-flowworkspace: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-flowworkspace): [arguments]: Avoid to have
a plain directory on the list of libraries to link.
 2020-12-09 12:12:36 +01:00
zimoun 26cf5eb568
gnu: r-hdf5array: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-hdf5array): [arguments]: Avoid to have a
plain directory on the list of libraries to link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:36 +01:00
zimoun b58c4e7613
gnu: r-cytolib: Fix r-rhdf5libs linking. 
* gnu/packages/bioconductor.scm (r-cytolib): [arguments]: Avoid to have a
plain directory on the list of libraries to link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:36 +01:00
Roel Janssen c5ae5c1c40
gnu: r-rhdf5lib: Fix build. 
* gnu/packages/bioconductor.scm (r-rhdf5lib)[arguments]: Fix build.
 2020-12-09 12:12:36 +01:00
zimoun 79cb6af375
gnu: r-rhdf5lib: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-rhdf5lib): Update to 1.12.0.
 2020-12-09 12:12:36 +01:00
zimoun 5992c25e7f
gnu: r-hdf5array: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-hdf5array): Update to 1.18.0.
 2020-12-09 12:12:36 +01:00
Roel Janssen c8da013780
gnu: Add r-matrixgenerics. 
* gnu/packages/bioconductor.scm (r-matrixgenerics): New variable.
 2020-12-09 12:12:36 +01:00
zimoun ed44a72acf
gnu: r-hitc: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-hitc): Update to 1.34.0.
 2020-12-09 12:12:35 +01:00
zimoun 7105658e9c
gnu: r-fithic: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-fithic): Update to 1.16.0.
 2020-12-09 12:12:35 +01:00
zimoun b6348b0edf
gnu: r-rgraphviz: Update to 2.34.0. 
* gnu/packages/bioconductor.scm (r-rgraphviz): Update to 2.34.0.
 2020-12-09 12:12:35 +01:00
zimoun 8fa30df02a
gnu: r-preprocesscore: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-preprocesscore): Update to 1.52.0.
 2020-12-09 12:12:35 +01:00
zimoun e5b2c80dc2
gnu: r-fourcseq: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-fourcseq): Update to 1.24.0.
 2020-12-09 12:12:35 +01:00
zimoun 3cacc3bdce
gnu: r-icens: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-icens): Update to 1.62.0.
 2020-12-09 12:12:35 +01:00
zimoun 126846a0da
gnu: r-m3c: Update to 1.12.0. 
* gnu/packages/bioconductor.scm (r-m3c): Update to 1.12.0.
 2020-12-09 12:12:35 +01:00
zimoun 7a242042ae
gnu: r-rgreat: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-rgreat): Update to 1.22.0.
 2020-12-09 12:12:35 +01:00
zimoun 15be98c136
gnu: r-biodist: Update to 1.62.0. 
* gnu/packages/bioconductor.scm (r-biodist): Update to 1.62.0.
 2020-12-09 12:12:34 +01:00
zimoun 7891c83c3e
gnu: r-biocworkflowtools: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-biocworkflowtools): Update to 1.16.0.
 2020-12-09 12:12:34 +01:00