diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 79 |
1 files changed, 55 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8aba7f1c5f..8dbcd5dd33 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7245,18 +7245,19 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.52.0") + (version "1.52.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "1wc7a953n6qrlh9azzg1q68rk99h3xkbs82wq0yk6h2vb2c5r3zk")))) + "0qwrsd9fcpkv7hhzy1scnj7ahdxi6cjary28kqk6b36gkzmnrw4r")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) ("r-graph" ,r-graph) ("r-rbgl" ,r-rbgl) ("r-rcurl" ,r-rcurl) @@ -7372,13 +7373,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0g06y6xlm2q7p7g7phfc8qj14pqpgbb0mkyjzkfgsrwjmzvpwy6m")))) + "1d64sh43pfc9vj2l7y7x6sb44l67wlnn3dzygp7ws0smn06mardq")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7452,13 +7453,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.3") + (version "3.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "12889lwcray2cw0skzy1xp1y3siiz6n5cwx8ni86m7r671p6zmb2")))) + "013glavk6a1wpyq3q35k343bdp6rf27w30q59i4kf47rp3i37g15")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7480,13 +7481,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1sd01yv1hnwc16412ilncrrph4gxsr9ds0nqg1czl69fqaixjn1i")))) + "144x3d3b9a3q5jy4aqrk1nf2yavwjhwlf71s7qyr4x3ms3wmvf8i")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7924,13 +7925,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.0") + (version "1.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "17jy7lrpdaafd8g5v6j70xsypi0lqljdqmhv9f2r1xpyg3yjd84p")))) + "02psq3jfgghdydwbydb1j792lvfg44l5npb44mx8d54ckr8658dd")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -9040,14 +9041,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.32.0") + (version "3.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "100jwi43y4xdqb5lldx1ld58jg9icdjgz6c7ylx95gspipnkbgjp")))) + "0jj6klfha5v5qmx2sjblf1an6s2zqd7mmgsp7sfmh4k2jpqi3jm9")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -9369,14 +9370,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.10.0") + (version "2.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1lqdlyvs2c9g55zf8gnw142ps4jid644fhfvclnax7sjjwrqdjzv")))) + "0z63yqazkycq0zbbarq9ida6al35hv3g7g9g7s7bss4gh0hk7lhd")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -10568,13 +10569,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0k4jc0xc2n49saylcjrg7laxq4mchg4nv06nrbc6cp4vzpf33jh5")))) + "16a17161xlhh6qpna9qxph3anlc7ydgyrczmy4alfiw8si7pzmxa")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10603,14 +10604,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.12.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "19cyjjzgmhswni6js4bhbj5djp976sl9n648kk7viazgkspql884")))) + "17mknpkvs7mgnlbf2hv9k7rwbx2vlg60yrwfyb8nn3nxsb6vm7yn")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12535,15 +12536,15 @@ once. This package provides tools to perform Drop-seq analyses.") (define-public pigx-rnaseq (package (name "pigx-rnaseq") - (version "0.0.5") + (version "0.0.6") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/" - "releases/download/v" version + "releases/download/v." version "/pigx_rnaseq-" version ".tar.gz")) (sha256 (base32 - "05gn658zpj9xki5dbs728z9zxq1mcm25hkwr5vzwqxsfi15l5f2l")))) + "1w7cwbbz1sbvbyqh5c60iqcjfs3qsppmdgxqa1i0w5wwb9mkh27m")))) (build-system gnu-build-system) (arguments `(#:parallel-tests? #f ; not supported @@ -12566,7 +12567,6 @@ once. This package provides tools to perform Drop-seq analyses.") ("trim-galore" ,trim-galore) ("htseq" ,htseq) ("samtools" ,samtools) - ("bedtools" ,bedtools) ("r-minimal" ,r-minimal) ("r-rmarkdown" ,r-rmarkdown) ("r-ggplot2" ,r-ggplot2) @@ -12603,7 +12603,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.40") + (version "0.0.41") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12611,7 +12611,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "0y9x62cfwzhsp82imnawyamxp58bcb00yjxdy44spylqnjdlsaj8")))) + "0akbxdmsjsq5fzbwaap04hqjpsfgv1l6yrc2pwgbya1xgqvcq6vy")))) (build-system gnu-build-system) ;; parts of the tests rely on access to the network (arguments '(#:tests? #f)) @@ -14754,3 +14754,34 @@ ATAC-seq results. It was written to make it easier to spot differences that might be caused by ATAC-seq library prep or sequencing. The main program, @code{ataqv}, examines aligned reads and reports some basic metrics.") (license license:gpl3+))) + +(define-public r-psiplot + (package + (name "r-psiplot") + (version "2.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kcha/psiplot.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08438h16cfry5kqh3y9hs8q1b1a8bxhblsm75knviz5r6q0n1jxh")))) + (build-system r-build-system) + (propagated-inputs + `(("r-mass" ,r-mass) + ("r-dplyr" ,r-dplyr) + ("r-tidyr" ,r-tidyr) + ("r-purrr" ,r-purrr) + ("r-readr" ,r-readr) + ("r-magrittr" ,r-magrittr) + ("r-ggplot2" ,r-ggplot2))) + (home-page "https://github.com/kcha/psiplot") + (synopsis "Plot percent spliced-in values of alternatively-spliced exons") + (description + "PSIplot is an R package for generating plots of @dfn{percent +spliced-in} (PSI) values of alternatively-spliced exons that were computed by +vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots +are generated using @code{ggplot2}.") + (license license:expat))) |