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Author SHA1 Message Date
Ricardo Wurmus
5b27dbb67e
gnu: r-dexseq: Update to 1.54.1. 
* gnu/packages/bioconductor.scm (r-dexseq): Update to 1.54.1.

Change-Id: I52f24353dbf1ee9160f17cc0c510a8a172b73905
 2025-05-13 14:50:12 +02:00
Ricardo Wurmus
b3d544ad7e
gnu: r-deseq2: Update to 1.48.1. 
* gnu/packages/bioconductor.scm (r-deseq2): Update to 1.48.1.

Change-Id: Ieb18674dab9b016f37b880a06f772fbbdbadddb7
 2025-05-13 14:50:12 +02:00
Ricardo Wurmus
b927cbe70d
gnu: Remove r-snapcgh. 
This package has been removed with the release of Bioconductor 3.19, and it
now fails to build.

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

Change-Id: Id4408ea2d17d07913fea359292eb3e5d7329b13d
 2025-05-12 08:55:51 +02:00
Ricardo Wurmus
f54467968d
gnu: r-tradeseq: Add missing input. 
* gnu/packages/bioconductor.scm (r-tradeseq)[native-inputs]: Add
r-delayedmatrixstats.
[properties]: Record it in updater-extra-native-inputs.

Change-Id: Icc877a48320083d2e5c4987643d52d60c9b11f05
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
3f3b2e31a8
gnu: r-screpertoire: Disable one more test. 
* gnu/packages/bioconductor.scm (r-screpertoire)[arguments]: Disable one more test.

Change-Id: I9d44fc50137f6e90f69a2e871a375aff192045ae
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
1ae270f125
gnu: r-scdd: Add missing input. 
* gnu/packages/bioconductor.scm (r-scdd)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-testthat.

Change-Id: Ibd0925b94ae82145055a0b2c5d53f38df202b077
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
9f17727fd5
gnu: r-classdiscovery: Update to 3.4.8. 
* gnu/packages/bioconductor.scm (r-classdiscovery): Update to 3.4.8.

Change-Id: I8d5c707ae55161cf93bf14ab3a4f87c40000327d
 2025-05-12 08:55:12 +02:00
Ricardo Wurmus
d247e988a8
gnu: r-metap: Update to 1.12. 
* gnu/packages/bioconductor.scm (r-metap): Update to 1.12.

Change-Id: Iad76b9dc0261cad250ed087e64c0490deecafd34
 2025-05-12 08:55:12 +02:00
Ricardo Wurmus
76ba63a8bd
gnu: r-ggpicrust2: Update to 2.1.2. 
* gnu/packages/bioconductor.scm (r-ggpicrust2): Update to 2.1.2.
[propagated-inputs]: Remove r-aldex2, r-circlize, r-deseq2, r-edger, r-ggally, r-lefser,
r-limma, r-maaslin2, r-metagenomeseq, r-microbiomestat, and
r-summarizedexperiment; add r-ggplotify, r-ggraph, r-magrittr,
r-progress, and r-tidygraph.
[native-inputs]: Add r-fgsea, r-ggvenndiagram, r-mockery, and r-upsetr.

Change-Id: I174ff92587f70e46d2c3520c0ff1bbf38e4b8172
 2025-05-12 08:55:12 +02:00
Ricardo Wurmus
94fa3ed421
gnu: r-scgate: Update to 1.7.0. 
* gnu/packages/bioconductor.scm (r-scgate): Update to 1.7.0.

Change-Id: I647cbfc4c289ba8a010e52732b6340856fe1d5b3
 2025-05-12 08:55:12 +02:00
Ricardo Wurmus
fc5e3b794a
gnu: r-pscbs: Update to 0.68.0. 
* gnu/packages/bioconductor.scm (r-pscbs): Update to 0.68.0.
[propagated-inputs]: Remove r-listenv.
[native-inputs]: Remove r-r-devices.

Change-Id: Ib198ca104b43c77790c258e8c53fcc34f2b521a1
 2025-05-12 08:55:12 +02:00
Ricardo Wurmus
1a5c48351e
gnu: r-dsb: Update to 2.0.0. 
* gnu/packages/bioconductor.scm (r-dsb): Update to 2.0.0.
[native-inputs]: Add r-spelling.

Change-Id: I1fdebc33bb8a57057b5b8a2ab8b4e401e5631c97
 2025-05-12 08:55:12 +02:00
Ricardo Wurmus
880c0191a5
gnu: r-dmrcate: Update to 3.4.0. 
* gnu/packages/bioconductor.scm (r-dmrcate): Update to 3.4.0.

Change-Id: I60622a7c030ec5005a7decaf6f0e8cd77023b715
 2025-05-12 08:55:11 +02:00
Ricardo Wurmus
7597115cc9
gnu: r-sesamedata: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-sesamedata): Update to 1.26.0.

Change-Id: I3ed54ced025597402321b550808686ad2d9175bd
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
5cae934a8c
gnu: r-rtcga-rnaseq: Update to 20151101.38.0. 
* gnu/packages/bioconductor.scm (r-rtcga-rnaseq): Update to 20151101.38.0.

Change-Id: I5152b9bca7c12d968bbdf95a84b8874134f15b11
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
14f8453677
gnu: r-rnbeads-hg19: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-rnbeads-hg19): Update to 1.40.0.

Change-Id: I37638d96b655cd1c91769d9e6ba332ae09695c39
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
d2ab8c7909
gnu: r-rnaseqdata-hnrnpc-bam-chr14: Update to 0.46.0. 
* gnu/packages/bioconductor.scm (r-rnaseqdata-hnrnpc-bam-chr14): Update to 0.46.0.

Change-Id: I6032eec74f1b93c4b44492b03fbcf270999f4cae
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
e9dacafe12
gnu: r-parathyroidse: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-parathyroidse): Update to 1.46.0.

Change-Id: I3408aa5f9e5d5f0f67520e18b34989621d419497
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
a2958d750b
gnu: r-curatedtcgadata: Update to 1.30.0. 
* gnu/packages/bioconductor.scm (r-curatedtcgadata): Update to 1.30.0.

Change-Id: Ia427cb0b63ba1089d717e7efdb73ff8826bcf07d
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
ef204b63e1
gnu: r-gagedata: Update to 2.46.0. 
* gnu/packages/bioconductor.scm (r-gagedata): Update to 2.46.0.

Change-Id: I5fc2489891207fbb249651d0b56eff7c75274cca
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
7bcd5c266b
gnu: r-prolocdata: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-prolocdata): Update to 1.46.0.

Change-Id: I87cd79a11f9a1de302b7c3b7314918964a0c0143
 2025-05-12 08:55:10 +02:00
Ricardo Wurmus
280a808407
gnu: r-minionsummarydata: Update to 1.38.0. 
* gnu/packages/bioconductor.scm (r-minionsummarydata): Update to 1.38.0.

Change-Id: I978ac23b9ae0c69873d569d64cbce2a40b9b919e
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
b4036c29e3
gnu: r-minfidataepic: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-minfidataepic): Update to 1.34.0.

Change-Id: I5eac84d1db0b985140ff85bd580379405f1af78d
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
2b72597f1d
gnu: r-mousegastrulationdata: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-mousegastrulationdata): Update to 1.22.0.

Change-Id: I716e7325f77c65cc61f0914ef5ac5bb98e9f6410
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
eb298a4517
gnu: r-methylclockdata: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-methylclockdata): Update to 1.16.0.

Change-Id: Ie97c9e54f2a60b5132f2fd4f08d60602e0ff23d5
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
c9763f059f
gnu: r-methylaiddata: Update to 1.40.0. 
* gnu/packages/bioconductor.scm (r-methylaiddata): Update to 1.40.0.

Change-Id: I27fe623dde66a088b9567a6c459c03d6c4d822ca
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
7b52d2c776
gnu: r-macrophage: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-macrophage): Update to 1.24.0.

Change-Id: I9f7cd0b50543930a4c06f5f0d0067af1d6c82483
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
d6d559c4ab
gnu: r-golubesets: Update to 1.50.0. 
* gnu/packages/bioconductor.scm (r-golubesets): Update to 1.50.0.

Change-Id: I84daae58a4d84b578f0881cd5a7346966530de99
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
9046e17e02
gnu: r-genelendatabase: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-genelendatabase): Update to 1.44.0.

Change-Id: I834018e74e1ef8ca5c21003a1eb30bbe9c9997d8
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
30bec76b00
gnu: r-derfinderdata: Update to 2.26.0. 
* gnu/packages/bioconductor.scm (r-derfinderdata): Update to 2.26.0.

Change-Id: I9db140c44040670c4c2e44a8aaef2b65c24e2831
 2025-05-12 08:55:09 +02:00
Ricardo Wurmus
7bc427ff5d
gnu: r-chromstardata: Update to 1.34.0. 
* gnu/packages/bioconductor.scm (r-chromstardata): Update to 1.34.0.

Change-Id: I77f041f59bef6f1746a2898f92f874b65eed6f22
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
d32ed19654
gnu: r-celldex: Update to 1.18.0. 
* gnu/packages/bioconductor.scm (r-celldex): Update to 1.18.0.

Change-Id: I26e32649ebdf8400cf6157b90a548db3b8040ad9
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
aa3d171fee
gnu: r-breastcancervdx: Update to 1.46.0. 
* gnu/packages/bioconductor.scm (r-breastcancervdx): Update to 1.46.0.

Change-Id: I5c9913b28bd9bd7742c45f253b045855342fe443
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
a959047757
gnu: r-bodymaprat: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-bodymaprat): Update to 1.24.0.

Change-Id: I8ffbff5971e28cbe660c3722ccac85a981e1d789
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
9ddfef3a4a
gnu: r-bcellviper: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-bcellviper): Update to 1.44.0.

Change-Id: I916361d424274ddddfcb4b41b7df232278293e97
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
45244ba92e
gnu: r-airway: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-airway): Update to 1.28.0.

Change-Id: Ieb1826ed0355850310f2afb6e50ff7c320d1d19d
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
3ca5b6b7c4
gnu: r-adductdata: Update to 1.24.0. 
* gnu/packages/bioconductor.scm (r-adductdata): Update to 1.24.0.

Change-Id: I470854bac0f9a3f5080f591ad79a934e0b571cda
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
667a7fcd75
gnu: r-phyloseq: Update to 1.52.0. 
* gnu/packages/bioconductor.scm (r-phyloseq): Update to 1.52.0.

Change-Id: Ic5ef1e540aeedcedc25ca3aec6eaec0d7a72a7cb
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
409b2d0bb1
gnu: r-tximeta: Update to 1.26.0. 
* gnu/packages/bioconductor.scm (r-tximeta): Update to 1.26.0.
[native-inputs]: Add r-edger and r-org-dm-eg-db.

Change-Id: I2cc72379c43598ee838cddc06fda7a4930007b76
 2025-05-12 08:55:08 +02:00
Ricardo Wurmus
b6d5e929a9
gnu: r-tricycle: Update to 1.16.0. 
* gnu/packages/bioconductor.scm (r-tricycle): Update to 1.16.0.

Change-Id: I1c56fa881495a11f84eec0b1fe0b968c8cb29e50
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
1377add8f8
gnu: r-tcgabiolinks: Update to 2.36.0. 
* gnu/packages/bioconductor.scm (r-tcgabiolinks): Update to 2.36.0.

Change-Id: I9569c4178e12c45a1b07e2baed3137de3be531ce
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
06d3f0a265
gnu: r-biscuiteer: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-biscuiteer): Update to 1.22.0.

Change-Id: I74e038980d8e1ca20e12ad56341e18b3579f7372
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
7e1bebca15
gnu: r-omicade4: Update to 1.48.0. 
* gnu/packages/bioconductor.scm (r-omicade4): Update to 1.48.0.

Change-Id: I5b38a7ad1fc480c1accdb0b155f6fed989a0d648
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
c77aff235c
gnu: r-dmrseq: Update to 1.28.0. 
* gnu/packages/bioconductor.scm (r-dmrseq): Update to 1.28.0.

Change-Id: I6692b4e87fd6169e9c10a261a718d4fb0df06fec
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
6f3e73c5e8
gnu: r-dada2: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-dada2): Update to 1.36.0.

Change-Id: I16732f2da9af2382fd3f557d005792616685a92e
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
f26f01e9fd
gnu: r-bsseq: Update to 1.44.0. 
* gnu/packages/bioconductor.scm (r-bsseq): Update to 1.44.0.
[propagated-inputs]: Add r-assorthead.
[native-inputs]: Add r-doparallel and r-matrix.

Change-Id: I94a78e4883893ac72d538be11fd480d8d33d20ed
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
f1e1492ae8
gnu: r-biotmle: Update to 1.32.0. 
* gnu/packages/bioconductor.scm (r-biotmle): Update to 1.32.0.
[native-inputs]: Add r-superlearner.

Change-Id: Ie97429835fd74ab0f721315be74cfe22794c2ae9
 2025-05-12 08:55:07 +02:00
Ricardo Wurmus
51bd87234a
gnu: r-biotip: Update to 1.22.0. 
* gnu/packages/bioconductor.scm (r-biotip): Update to 1.22.0.

Change-Id: Id60b2575a1be93eb5a079fed319f04d5300a3c95
 2025-05-12 08:55:06 +02:00
Ricardo Wurmus
68505b3f0e
gnu: r-bioqc: Update to 1.36.0. 
* gnu/packages/bioconductor.scm (r-bioqc): Update to 1.36.0.

Change-Id: Ifa044f66a99e146c89c78fe20a92ed277b9f58b6
 2025-05-12 08:55:06 +02:00
Ricardo Wurmus
85e3a70aef
gnu: r-bionet: Update to 1.68.0. 
* gnu/packages/bioconductor.scm (r-bionet): Update to 1.68.0.

Change-Id: I9d409cbb81002267a513d58298f3ebd7d6c1807b
 2025-05-12 08:55:06 +02:00