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128739 Commits (280162165b6d0fc66c0f7aa6fb6cf258a7c0673d)

Author SHA1 Message Date
Ricardo Wurmus 280162165b
gnu: r-mscoreutils: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-mscoreutils): Update to 1.14.1.

Change-Id: Ia978e23f1f0bf5a58ffa2c76a65c5f9982629aac
 2023-12-15 17:47:42 +01:00
Ricardo Wurmus 2f14829a7c
gnu: r-sparsearray: Update to 1.2.2. 
* gnu/packages/bioconductor.scm (r-sparsearray): Update to 1.2.2.

Change-Id: I96f367bf5c39c973e1c5fad3b9620bfcaf88417a
 2023-12-15 17:47:41 +01:00
Ricardo Wurmus aa3e41026a
gnu: r-scater: Update to 1.30.1. 
* gnu/packages/bioconductor.scm (r-scater): Update to 1.30.1.

Change-Id: I5e497b654bc4a26adc6d956f728f31ae631a239c
 2023-12-15 17:47:41 +01:00
Ricardo Wurmus 2fb96bed75
gnu: r-s4vectors: Update to 0.40.2. 
* gnu/packages/bioconductor.scm (r-s4vectors): Update to 0.40.2.

Change-Id: I6201d17fa2a6be618feb26ad632b9249f87d86c5
 2023-12-15 17:47:41 +01:00
Ricardo Wurmus ccf2d49837
gnu: r-ucell: Update to 2.6.2. 
* gnu/packages/bioconductor.scm (r-ucell): Update to 2.6.2.

Change-Id: Ie08960a237ad1515332794b23c2bd31e94299dfe
 2023-12-15 17:47:41 +01:00
Ricardo Wurmus be56597c9d
gnu: r-variancepartition: Update to 1.32.2. 
* gnu/packages/bioconductor.scm (r-variancepartition): Update to 1.32.2.
[propagated-inputs]: Add r-matrixstats.

Change-Id: I436a1db36ad910aec0fac87150c62735f6509575
 2023-12-15 17:47:41 +01:00
Ricardo Wurmus bb64a047b4
gnu: r-flowworkspace: Update to 4.14.1. 
* gnu/packages/bioconductor.scm (r-flowworkspace): Update to 4.14.1.

Change-Id: I2e950e77842add2eebeeffac2492ba0ef1aa6422
 2023-12-15 17:47:40 +01:00
Ricardo Wurmus 2ab52103c9
gnu: r-xcms: Update to 4.0.1. 
* gnu/packages/bioconductor.scm (r-xcms): Update to 4.0.1.

Change-Id: I98dd730bb959d2483164177a3e534915d13fee44
 2023-12-15 17:47:40 +01:00
Ricardo Wurmus e22fc284e3
gnu: r-genomicscores: Update to 2.14.2. 
* gnu/packages/bioconductor.scm (r-genomicscores): Update to 2.14.2.

Change-Id: I00417ef0c2f9657ec39690baa52a1cd075fb69c6
 2023-12-15 17:47:40 +01:00
Ricardo Wurmus 0d5917604c
gnu: r-dose: Update to 3.28.2. 
* gnu/packages/bioconductor.scm (r-dose): Update to 3.28.2.
[propagated-inputs]: Remove r-hpo-db and r-mpo-db; add r-yulab-utils.

Change-Id: Ia29d318cac9b1e261fb89fc4d15f8b40ec3583f3
 2023-12-15 17:47:40 +01:00
Ricardo Wurmus cff731dae5
gnu: r-lefser: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-lefser): Update to 1.12.1.

Change-Id: Iac94395b267e925116929d48abb3c28cff31504e
 2023-12-15 17:47:39 +01:00
Ricardo Wurmus fcdd57e5fe
gnu: r-zellkonverter: Update to 1.12.1. 
* gnu/packages/bioconductor.scm (r-zellkonverter): Update to 1.12.1.

Change-Id: I0db7450b3eff32e739ea3b806dde96114caba440
 2023-12-15 17:47:39 +01:00
Ricardo Wurmus 01f345225b
gnu: r-variantannotation: Update to 1.48.1. 
* gnu/packages/bioconductor.scm (r-variantannotation): Update to 1.48.1.

Change-Id: I51e6a6db61fc4782823f9a7f85345742b8c7ab72
 2023-12-15 17:47:39 +01:00
Ricardo Wurmus 69126c2b9c
gnu: r-trackviewer: Update to 1.38.1. 
* gnu/packages/bioconductor.scm (r-trackviewer): Update to 1.38.1.

Change-Id: I3ec74e7c37830e7a0b3b12311e304cc2e4fe322e
 2023-12-15 17:47:39 +01:00
Ricardo Wurmus 5a231ed554
gnu: r-tcgautils: Update to 1.22.2. 
* gnu/packages/bioconductor.scm (r-tcgautils): Update to 1.22.2.

Change-Id: I9c33a55076c672fa3a6ff6c97675dee16d186a39
 2023-12-15 17:47:38 +01:00
Ricardo Wurmus 27fab6cfee
gnu: r-rhdf5filters: Update to 1.14.1. 
* gnu/packages/bioconductor.scm (r-rhdf5filters): Update to 1.14.1.

Change-Id: I260973b51c3a8e895339d1c4b6fbed8f66ccb50c
 2023-12-15 17:47:38 +01:00
Ricardo Wurmus be49fe22cd
gnu: r-rhdf5: Update to 2.46.1. 
* gnu/packages/bioconductor.scm (r-rhdf5): Update to 2.46.1.

Change-Id: Ia4781476ab82dd867a707e98767d8ee12d208003
 2023-12-15 17:47:38 +01:00
Ricardo Wurmus 0f499ab3b0
gnu: r-msnbase: Update to 2.28.1. 
* gnu/packages/bioconductor.scm (r-msnbase): Update to 2.28.1.

Change-Id: I25fdd2662ab60939732cdee51fc2b53916f1d705
 2023-12-15 17:47:38 +01:00
Ricardo Wurmus 5883f6d17f
gnu: r-genomeinfodb: Update to 1.38.2. 
* gnu/packages/bioconductor.scm (r-genomeinfodb): Update to 1.38.2.

Change-Id: I17852db375cc7e833d100998c89751e68f3d4362
 2023-12-15 17:47:38 +01:00
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 93597fc39c
gnu: pyscenic: Update to 0.11.2-1.5f170fd. 
* gnu/packages/bioinformatics.scm (pyscenic): Update to 0.11.2-1.5f170fd.
[build-system]: Use pyproject-build-system.
[arguments]: Patch setup.py.
[propagated-inputs]: Add python-pyarrow.

Change-Id: I3acd7c921c2c44741c0afd0bbda011f63ed14c42
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 46b1e717cf
gnu: python-ctxcore: Update to 0.2.0. 
* gnu/packages/bioinformatics.scm (python-ctxcore): Update to 0.2.0.
[build-system]: Use pyproject-build-system.
[propagated-inputs]: Replace python-pyarrow-0.16 with python-pyarrow.

Change-Id: I3f72f9872b438c0a624d23becb5d7828f1986da7
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus b2aa1d7cd0
gnu: r-readwriter: Update to 1.5.3-1.91373c4. 
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 1.5.3-1.91373c4.
[propagated-inputs]: Remove r-gdata.

Change-Id: Ice16d3b07d7446ca864fd30e46110c9060b83081
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 07f85bb057
gnu: r-stringendo: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (r-stringendo): Update to 0.6.0.
[propagated-inputs]: Remove r-devtools and r-usethis; add r-clipr.

Change-Id: Iff4a841beb51558ba7d5d8e87ee56e7c3f2b2710
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 4d92caef51
gnu: r-liana: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-liana)[propagated-inputs]: Add r-basilisk
and r-basilisk-utils.

Change-Id: I5dce058a446245e6797cca1c35485f38b3da819a
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 0ec25720ab
gnu: python-vaex-core: Add missing input. 
* gnu/packages/python-science.scm (python-vaex-core)[propagated-inputs]: Add
python-click.

Change-Id: Id91e925832ed107d5b346ba513a9825dc31481f6
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 07acdb1552
gnu: r-desctools: Update to 0.99.52. 
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.52.
[propagated-inputs]: Remove r-bh; add r-cli.

Change-Id: Idca54e4796494b1d5635412c8f15bf639383ee0a
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 3e17f2ff9c
gnu: r-bayesfactor: Update to 0.9.12-4.6. 
* gnu/packages/statistics.scm (r-bayesfactor): Update to 0.9.12-4.6.

Change-Id: Iac17532bb38081a536790af3c5a36ad4791905b9
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 53082f702d
gnu: r-cairo: Update to 1.6-2. 
* gnu/packages/statistics.scm (r-cairo): Update to 1.6-2.

Change-Id: I519f1bef619873d81c38b272251075b4c8c88c68
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 040c86f2c8
gnu: r-tclust: Update to 1.5-5. 
* gnu/packages/statistics.scm (r-tclust): Update to 1.5-5.

Change-Id: I8526d099efd09fc458deb4feb090eb83671549ea
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 541d828f97
gnu: r-robust: Update to 0.7-3. 
* gnu/packages/statistics.scm (r-robust): Update to 0.7-3.

Change-Id: Ia4908566898547b7d8d14138f776de78f8f4a9fd
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 01c7baaf43
gnu: r-pcapp: Update to 2.0-4. 
* gnu/packages/statistics.scm (r-pcapp): Update to 2.0-4.

Change-Id: Ie0ad4cd7ddf9c649294f4ba76fc3aa6422f5e81c
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus a5df4d20ee
gnu: r-robustbase: Update to 0.99-1. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-1.

Change-Id: I01fe9d9a24471eaa93439169ad197fbaf54a8446
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus 45e59dae8f
gnu: r-mclust: Update to 6.0.1. 
* gnu/packages/statistics.scm (r-mclust): Update to 6.0.1.

Change-Id: Iabc63d21f904d92205db4364053537f580658af5
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus f7da625a37
gnu: r-diptest: Update to 0.77-0. 
* gnu/packages/statistics.scm (r-diptest): Update to 0.77-0.

Change-Id: Ic0dcd061fc82a6ef5bc4eb9d222245c00052e0aa
 2023-12-15 16:13:14 +01:00
Ricardo Wurmus c5e8b34bde
gnu: r-fastica: Update to 1.2-4. 
* gnu/packages/statistics.scm (r-fastica): Update to 1.2-4.

Change-Id: Ia0f61d080891317f825837e42aee70e94eff83dc
 2023-12-15 16:13:14 +01:00