diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 155 |
1 files changed, 113 insertions, 42 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a85cf904f7..ea8a885c5f 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2154,13 +2154,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.48.2") + (version "2.48.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1na271z9gc3b7xfcghbljj9lqq6v9b2kb71xahsq544yv4z9w8xj")))) + "096s243yzbhhz3wsm7azml5sznqczmcpi5g0gnb02mah1przczfx")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -2247,13 +2247,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.60.1") + (version "2.60.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1a2vq4rram7chnccx0piccgi0mlblmjh26y51bch86lxr7qwlr22")))) + "0ai0fg0w4l0a7avbafdbqjgjpg91myxalwrg2i3ixm1l2lyyfyah")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -2743,14 +2743,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.16.3") + (version "2.16.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1y3d6mx59531ixr8nzq57sa5nwimq3qyy1xabk52vvdbkl2aa52x")))) + "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3007,13 +3007,13 @@ alignments.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.44.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0y7lnvfcfrs72xbkn67xcqyz9csl5696mr2zl425fkhmnmimm4fg")))) + "0byizkq18kkyq3n604f38z4mikhi3szsrfrlz22wdq2ldq3nzkis")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -3300,13 +3300,13 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-limma (package (name "r-limma") - (version "3.48.1") + (version "3.48.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1wscxvhrz16sfa0qwk9anxqjy1vgvqmq6ia9gx6pwpga8qzwn5bi")))) + "0385ac0hvvml99krcgcpp6q7layjhzgp9xcxkcjrpfg5mjg1z4sx")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -3987,13 +3987,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.52.0") + (version "1.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0iic0g0clsjd9ypdmfs6k52hrnmfszhxzg0xx89nszpasf69wghv")))) + "11w6dx09pb49lin1gr9q88xn7ixh9jd5z6m9z27djchm0nw10lx9")))) (build-system r-build-system) (arguments `(#:phases @@ -4221,24 +4221,28 @@ graph construction.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.8.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 "13q6zbdkpx1iw6n75pggg50f9q3zb7k3dxjdra8mhi6zin7018j8")))) + (base32 "04ac4mjh3pgdlws0aiacqg0vd7bhg890w44r7b90p947c3rk1mfw")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) ("r-dplyr" ,r-dplyr) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfeatures" ,r-genomicfeatures) ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) ("r-rlang" ,r-rlang) ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) ("r-variantannotation" ,r-variantannotation))) (native-inputs `(("r-knitr" ,r-knitr))) @@ -4767,14 +4771,14 @@ signal in the input, that lead to spurious peaks during peak calling.") (define-public r-diffbind (package (name "r-diffbind") - (version "3.2.4") + (version "3.2.5") (source (origin (method url-fetch) (uri (bioconductor-uri "DiffBind" version)) (sha256 (base32 - "024ff12v42yvcma29cis4f777jrdgmgfr06lxn6l3nh30ghxawci")))) + "1rp4sgx58g1lq5brpx07wffllhvsqq1097vrjiaksbih08338nih")))) (properties `((upstream-name . "DiffBind"))) (build-system r-build-system) (propagated-inputs @@ -5013,14 +5017,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.26.2") + (version "3.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "003550ygh0haxyyypsss7s03jlsx7cqkhly4fcz10maczi6j4l30")))) + "07dvg3r4kghkqhh1a8rw149hgfswmzdh9cvnam8c82006cpmi74s")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -5067,13 +5071,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "1xq3a9ls125wfnhn13rdbsxzq3f6klsspx7h0znd6l67f5j5k25s")))) + "0kjsc5ghcplay4a74ffpwsf3kbp51x6rl5265gvlfchdwrawkzd2")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -5685,14 +5689,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "0ypl4h80m08sf7r4zfvqgvpsz46x15wvcl1idq5pd813bp1w2sws")))) + "1y60yvg1rl21cab9xrkns0209pg44mwr90qj099dvk97wsjkx67g")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -5717,14 +5721,14 @@ platform for merging tree with associated data and converting file formats.") (define-public r-ggtree (package (name "r-ggtree") - (version "3.0.2") + (version "3.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ggtree" version)) (sha256 (base32 - "0i665b5jxgsv3ncxmczy7n0h911br44dw9f7m4jwv3pjmr5mm6vk")))) + "02ydi5iyxwrvwfjmv8pbanmzpi1r99mc4gxl17fpq2jf1d1mk6g0")))) (properties `((upstream-name . "ggtree"))) (build-system r-build-system) (propagated-inputs @@ -6241,14 +6245,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1xm204wp3m3mmlc1s59lscbbjvwm5nj32vvf16njcg7pb32lsiqa")))) + "1bkk69b5llkmvmpsnhymwjm2szmzypgszfsw8mak1b5ms5zf8lr0")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -7242,14 +7246,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.18.1") + (version "3.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "1g3llrb51m8lj3prcr6ryxj0lf4qqzg9mzi36y71pp9qzfvf3c0k")))) + "0kp6j42mpxrpd02cjrzqmrx3rvvpi90xiy4gc5km6ny3vxbhlaqw")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -7314,14 +7318,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.0.2") + (version "4.0.4") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "11pjzh7inh1x0gry42nlq4har65s8pc0w3bkccm6kmxycvaxb9rh")))) + "161w9mn2plmymvzf1hkk9fwi3d9c26kbcpndyyrfcl6bg2nxr1s8")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -10877,14 +10881,14 @@ data.") (define-public r-universalmotif (package (name "r-universalmotif") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "universalmotif" version)) (sha256 (base32 - "1hwp7802r4pr7yafzir9afqaim9l0vznglm35b0gxaca8k7a3jvy")))) + "0hv2v2zgif5ihr5hxmdz32rln43jc1j0rslp44kd3rijjl45zysn")))) (properties `((upstream-name . "universalmotif"))) (build-system r-build-system) @@ -11843,14 +11847,14 @@ analytics on packages.") (define-public r-biocset (package (name "r-biocset") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocSet" version)) (sha256 (base32 - "18zr0r4b4rblfmsiilipqdfxn9fgymx75hlxzx1wk3bm71ryk078")))) + "0nmrg9cgq8l9w467y364jghnvym05abpj8pyj90grmrib2xc5sj2")))) (properties `((upstream-name . "BiocSet"))) (build-system r-build-system) (propagated-inputs @@ -12469,14 +12473,14 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "16p6shab4y8sy1adn4qr05ysvwmvs9idliccixafvx9icv5sla86")))) + "06bpfpddsl49csxrs8hlx5pv0absc2wdcparchf8qqaqydazwci2")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -12704,14 +12708,14 @@ libraries.") (define-public r-scuttle (package (name "r-scuttle") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scuttle" version)) (sha256 (base32 - "1vxmgm52n5z2m1a7d4c5ajp5d35rdq7j3hln9qn7188zk9ijjsz5")))) + "015k879gg2r39lp6mz26jwmysa56k0ial6v74zzmbi8hnz9zic3i")))) (properties `((upstream-name . "scuttle"))) (build-system r-build-system) (propagated-inputs @@ -12822,14 +12826,14 @@ variable and significantly correlated genes.") (define-public r-sparsematrixstats (package (name "r-sparsematrixstats") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "sparseMatrixStats" version)) (sha256 (base32 - "0ilspddfkqpnf2lng9jjs2ahv6vlc6sap69fzkcw314rha59kncr")))) + "0b22kzg751zlkcbs8pi0bcqrsj3imsg35qfvxfrqb7gav7qznc8v")))) (properties `((upstream-name . "sparseMatrixStats"))) (build-system r-build-system) @@ -12850,14 +12854,14 @@ data in the column sparse format.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.14.0") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "02r68rzmc54m353fpw5ampyv26i5622bc7iihfqlpy6p3033lpqk")))) + "1avzd3fj4am9klmlx03nwq2pvgx7646yjwha1gqf0cbx5hibxy02")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -13662,6 +13666,73 @@ starting site, start codon, stop codon and transcription ending site.") visualizations for publication-quality multi-panel figures.") (license license:gpl2+))) +(define-public r-ballgown + (package + (name "r-ballgown") + (version "2.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ballgown" version)) + (sha256 + (base32 + "0ff8z4pfgzai2q4aafclg36bhsi9jwl9xhh1p9fqhmikisscq7i1")))) + (properties `((upstream-name . "ballgown"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-sva" ,r-sva))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/ballgown") + (synopsis "Flexible, isoform-level differential expression analysis") + (description + "This package provides tools for statistical analysis of assembled +transcriptomes, including flexible differential expression analysis, +visualization of transcript structures, and matching of assembled transcripts +to annotation.") + (license license:artistic2.0))) + +(define-public r-megadepth + (package + (name "r-megadepth") + (version "1.2.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "megadepth" version)) + (sha256 + (base32 + "0grgj7bzyqnxby0sx5ic1h9bzmx19xwl0a5b3v6wbnwqcla2i3kg")))) + (properties `((upstream-name . "megadepth"))) + (build-system r-build-system) + (inputs `(("megadepth" ,megadepth))) + (propagated-inputs + `(("r-cmdfun" ,r-cmdfun) + ("r-dplyr" ,r-dplyr) + ("r-fs" ,r-fs) + ("r-genomicranges" ,r-genomicranges) + ("r-magrittr" ,r-magrittr) + ("r-readr" ,r-readr) + ("r-xfun" ,r-xfun))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/LieberInstitute/megadepth") + (synopsis "BigWig and BAM related utilities") + (description + "This package provides an R interface to Megadepth. It is particularly +useful for computing the coverage of a set of genomic regions across bigWig or +BAM files. With this package, you can build base-pair coverage matrices for +regions or annotations of your choice from BigWig files.") + (license license:artistic2.0))) + (define-public r-tximeta (package (name "r-tximeta") |