diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 135 |
1 files changed, 123 insertions, 12 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a7af5c42ce..d82a73ac51 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -59,6 +59,7 @@ #:use-module (gnu packages python) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) + #:use-module (gnu packages protobuf) #:use-module (gnu packages statistics) #:use-module (gnu packages tls) #:use-module (gnu packages web) @@ -157,6 +158,25 @@ descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.") (license license:artistic2.0))) +(define-public r-jaspar2020 + (package + (name "r-jaspar2020") + (version "0.99.10") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "JASPAR2020" version 'annotation)) + (sha256 + (base32 "0nrp63z7q2ivv5h87f7inpp2qll2dfgj4227l4rbnzii38a2vfdr")))) + (properties `((upstream-name . "JASPAR2020"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://jaspar.elixir.no/") + (synopsis "Data package for JASPAR database (version 2020)") + (description "Data package for JASPAR2020. To explore these databases, +utilize the TFBSTools package (version 1.23.1 or higher).") + (license license:gpl2))) + (define-public r-mafh5-gnomad-v3-1-2-grch38 (package (name "r-mafh5-gnomad-v3-1-2-grch38") @@ -1127,6 +1147,46 @@ Ensembl.") Ensembl.") (license license:artistic2.0))) +(define-public r-escape + (package + (name "r-escape") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "escape" version)) + (sha256 + (base32 "0bmin69ax7l5x3a0k9mv183277a0hl4znx02y79v2ilkgqkdm7fn")))) + (properties `((upstream-name . "escape"))) + (build-system r-build-system) + (propagated-inputs (list r-biocparallel + r-broom + r-data-table + r-dplyr + r-ggplot2 + r-ggridges + r-gseabase + r-gsva + r-matrix + r-matrixgenerics + r-msigdbr + r-patchwork + r-reshape2 + r-rlang + r-singlecellexperiment + r-stringr + r-summarizedexperiment + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/escape") + (synopsis "Single cell analysis platform for enrichment") + (description + "R-escape streamlines gene set enrichment analysis for single-cell RNA +sequencing. Using raw count information, Seurat objects, or +@code{SingleCellExperiment} format, users can perform and visualize GSEA +across individual cells.") + (license license:gpl2))) + (define-public r-snplocs-hsapiens-dbsnp144-grch37 (package (name "r-snplocs-hsapiens-dbsnp144-grch37") @@ -5599,6 +5659,35 @@ identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.") (license license:gpl3))) +;; This is a CRAN package, but it depends on r-limma from Bioconductor. +(define-public r-dsb + (package + (name "r-dsb") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "dsb" version)) + (sha256 + (base32 "1xzhd4q04c1vql49r6m4zskpx7f5hkl5hmdgr3gsbxb73xfs51v2")))) + (properties `((upstream-name . "dsb"))) + (build-system r-build-system) + (propagated-inputs (list r-limma r-magrittr r-mclust)) + (native-inputs (list r-knitr r-rmarkdown)) + (home-page "https://github.com/niaid/dsb") + (synopsis + "Normalize & denoise droplet single cell protein data (CITE-Seq)") + (description + "R-dsb improves protein expression analysis in droplet-based single-cell +studies. The package specifically addresses noise in raw protein UMI counts +from methods like CITE-seq. It identifies and removes two main sources of +noise—protein-specific noise from unbound antibodies and droplet/cell-specific +noise. The package is applicable to various methods, including CITE-seq, +REAP-seq, ASAP-seq, TEA-seq, and Mission Bioplatform data. Check the vignette +for tutorials on integrating dsb with Seurat and Bioconductor, and using dsb +in Python.") + (license license:cc0))) + (define-public r-dss (package (name "r-dss") @@ -7324,13 +7413,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.5") + (version "4.0.6") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "16cghh83v14jdq5n6xkm3jxj87n6l6zrxjgqdwb2ffgc26vkpb7w")))) + "0vksak7rv0agar0gplpj2fcp3183l3iyvbqjmx64c7dwpzjh3lb5")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7668,13 +7757,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "06xa3dcdk6jprvpyvr3pfbv6qv8xrqw2n6rrfp8q8qizx3ifj431")))) + "0y54kdgb77xqni46pgff1by2ska2jaxfcpq6gk86wb2rym37wlxj")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -13131,14 +13220,14 @@ accessiblity for new Bioconductor users is hopefully increased.") (define-public r-inspect (package (name "r-inspect") - (version "1.31.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "INSPEcT" version)) (sha256 (base32 - "0c7bw9cnav41vals2scv2gh5mj5nx2mgzagdb8g99sprdqv5924n")))) + "04znack6p50cmc2qyk4hf45m6v70p0bv7h3xs87j0x0h4mb920ch")))) (properties `((upstream-name . "INSPEcT"))) (build-system r-build-system) (propagated-inputs @@ -13147,7 +13236,6 @@ accessiblity for new Bioconductor users is hopefully increased.") r-biocparallel r-deseq2 r-desolve - r-gdata r-genomeinfodb r-genomicalignments r-genomicfeatures @@ -13156,6 +13244,7 @@ accessiblity for new Bioconductor users is hopefully increased.") r-kernsmooth r-plgem r-proc + r-readxl r-rootsolve r-rsamtools r-rtracklayer @@ -13229,14 +13318,14 @@ samples.") (define-public r-biocneighbors (package (name "r-biocneighbors") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocNeighbors" version)) (sha256 (base32 - "0w7hd6w0lmj1jaaq9zd5gwnnpkzcr0byqm5q584wjg4xgvsb981j")))) + "0lvsw920i75di5pwq7yvk8wcxp01wrh7863xmwbrmk5jrvl3y4h4")))) (properties `((upstream-name . "BiocNeighbors"))) (build-system r-build-system) (propagated-inputs @@ -17668,9 +17757,31 @@ of the analyses while minimizing technical noise.") (uri (bioconductor-uri "cytolib" version)) (sha256 (base32 - "1r2slhzrp3gf45k5gknqgj3vjz7p0rx2yjzrbp020inj82fp4mgi")))) + "1r2slhzrp3gf45k5gknqgj3vjz7p0rx2yjzrbp020inj82fp4mgi")) + ;; Remove bundled boost sources + (modules '((guix build utils))) + (snippet + '(delete-file-recursively "src/boost")))) (properties `((upstream-name . "cytolib"))) (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'unbundle + (lambda _ + (substitute* "src/Makevars.in" + (("\\$\\(USERLIB\\): \\$\\{boost_fs_objs\\}") + "$(USERLIB):") + (("\\$\\{cytolib_objs\\} \\$\\{boost_fs_objs\\} \\$\\{boost_sys_objs\\}") + "${cytolib_objs}") + (("PKG_CPPFLAGS =") + "PKG_CPPFLAGS = -lboost_filesystem") + #; + (("^BOOSTFSLIB.*") + (string-append "BOOSTFSLIB=" + #$(this-package-input "boost") "/libboost_filesystem.so\n")))))))) + (inputs (list boost openblas protobuf zlib)) (native-inputs (list r-knitr)) (propagated-inputs @@ -21322,13 +21433,13 @@ libraries.") (define-public r-singler (package (name "r-singler") - (version "2.4.0") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleR" version)) (sha256 - (base32 "0s7m3qdbgrqaq93k6rvyj34h36kdjvppn9ilflrcaa5w498fzfhf")))) + (base32 "0zlv45diasff5ipxp99dddswclrzzdcmkqp278fm2cj7aibvb3sd")))) (properties `((upstream-name . "SingleR"))) (build-system r-build-system) (propagated-inputs |