diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 1162 |
1 files changed, 1097 insertions, 65 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a284ea8d41..25202410e5 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -40,6 +40,7 @@ #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages docker) #:use-module (gnu packages gcc) #:use-module (gnu packages graph) #:use-module (gnu packages graphviz) @@ -84,6 +85,31 @@ submit gene-specific information, or which are scheduled for intense sequence analysis.") (license license:artistic2.0))) +(define-public r-org-bt-eg-db + (package + (name "r-org-bt-eg-db") + (version "3.13.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri + "org.Bt.eg.db" + version + 'annotation)) + (sha256 + (base32 + "0pwvwyfah8fhvaxdc8zkp3lp1v4mchhzr84r3hb0jx97icdvhafi")))) + (properties `((upstream-name . "org.Bt.eg.db"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi))) + (home-page "https://bioconductor.org/packages/org.Bt.eg.db") + (synopsis "Genome wide annotation for Bovine") + (description + "This package provides genome wide annotations for Bovine, primarily +based on mapping using Entrez Gene identifiers.") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") @@ -487,6 +513,34 @@ information about the latest version of the Gene Ontologies.") several related annotation packages.") (license license:artistic2.0))) +(define-public r-mus-musculus + (package + (name "r-mus-musculus") + (version "1.3.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Mus.musculus" version 'annotation)) + (sha256 + (base32 + "143zdf83gbfqhy8jm9df7gzhw5q3a64jrjrxrzjf0zd76j8s8j6y")))) + (properties `((upstream-name . "Mus.musculus"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-go-db" ,r-go-db) + ("r-org-mm-eg-db" ,r-org-mm-eg-db) + ("r-organismdbi" ,r-organismdbi) + ("r-txdb-mmusculus-ucsc-mm10-knowngene" + ,r-txdb-mmusculus-ucsc-mm10-knowngene))) + (home-page "https://bioconductor.org/packages/Mus.musculus") + (synopsis "Annotation package for the Mus.musculus object") + (description + "This package contains the @code{Mus.musculus} object to access data +from several related annotation packages.") + (license license:artistic2.0))) + (define-public r-org-ce-eg-db (package (name "r-org-ce-eg-db") @@ -1060,6 +1114,32 @@ sequencing data.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-biscuiteerdata + (package + (name "r-biscuiteerdata") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biscuiteerData" version 'experiment)) + (sha256 + (base32 + "1d7zibjf0qccmdnzdxh7wy1h943yhnbf8zdix72486pvhzm124zj")))) + (properties + `((upstream-name . "biscuiteerData"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-curl" ,r-curl) + ("r-experimenthub" ,r-experimenthub))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biscuiteerData") + (synopsis "Data package for Biscuiteer") + (description + "This package contains default datasets used by the Bioconductor package +biscuiteer.") + (license license:gpl3))) + (define-public r-chromstardata (package (name "r-chromstardata") @@ -2154,13 +2234,13 @@ 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 +2327,13 @@ 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 +2823,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.16.2") + (version "2.16.4") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0mbdfxic2vkfwm6b16353zr0qg8ylwf1vrxry85j2lgzl1qyyras")))) + "15yllkxr6sj5pfvkvv285nk3q5374nzq1iz8ywmnrq910k3xagd8")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -3007,13 +3087,13 @@ 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 +3380,13 @@ 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") @@ -3814,14 +3894,14 @@ region sets and other genomic features.") (define-public r-reportingtools (package (name "r-reportingtools") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ReportingTools" version)) (sha256 (base32 - "0v6wzfswwcd1xdxgwa9gzlkmavr4p55jy11k84anh0rs0xx3dmmj")))) + "0wq9y649dh1am6djzz0xlz42428xsgw2bdx1dknhdw2xbydmmx47")))) (properties `((upstream-name . "ReportingTools"))) (build-system r-build-system) @@ -3987,13 +4067,13 @@ 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 +4301,28 @@ graph construction.") (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") - (version "1.8.0") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "StructuralVariantAnnotation" version)) (sha256 - (base32 - "10h63h1v87nvm3bfyr6dsjlbmzxf1vks30d0xz6q4hssqq9xlzgv")))) + (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 +4851,14 @@ 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 +5097,14 @@ determining dependencies between variables, code improvement suggestions.") (define-public r-chippeakanno (package (name "r-chippeakanno") - (version "3.26.0") + (version "3.26.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ChIPpeakAnno" version)) (sha256 (base32 - "1wnmsdrb4wz2qprj5mnd3h0wx32y2mpy3xg7mjbgwlqn9bzpw3gk")))) + "07dvg3r4kghkqhh1a8rw149hgfswmzdh9cvnam8c82006cpmi74s")))) (properties `((upstream-name . "ChIPpeakAnno"))) (build-system r-build-system) (propagated-inputs @@ -5067,13 +5151,13 @@ 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 +5769,14 @@ 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 +5801,14 @@ 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 +6325,14 @@ 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 @@ -6541,14 +6625,14 @@ distributions.") (define-public r-scone (package (name "r-scone") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scone" version)) (sha256 (base32 - "1wlky6nkdpz8fya81l6zaxlxc30wyp2gkyh94y5995jwddll38z5")))) + "0zw8g4mql7b02xqwhc1i0bnhm20c1q9xqc7yz84j98pqbi996vi5")))) (build-system r-build-system) (propagated-inputs `(("r-aroma-light" ,r-aroma-light) @@ -7128,14 +7212,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.18.0") + (version "2.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1fzmaxjzyvq6xj5ny1sjijdwi4krzjgyaz52fczpwrxijq5pnyn1")))) + "00dbgkiv9x7g2i0anzcxpycwqqqry0y7jl3ad93lhvi31qnqq1sm")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -7242,14 +7326,14 @@ 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 +7398,14 @@ 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) @@ -7795,12 +7879,12 @@ frequency matrices from nine public sources, for multiple organisms.") (define-public r-motifbreakr (package (name "r-motifbreakr") - (version "2.6.0") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "motifbreakR" version)) (sha256 - (base32 "0i18qriznad4lr6ynzmz01k5yavs5m3h7hd0adbyg8lppbzm6hh4")))) + (base32 "1n6v8a7c27aswmbrlcwcpghf27aplkc6nn923imglc3c0sh2lkrz")))) (properties `((upstream-name . "motifbreakR"))) (build-system r-build-system) (propagated-inputs @@ -8612,14 +8696,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.14.0") + (version "3.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "1fs72lkgz1jik1smi6bb4f8jh6rrlpxdh3a5hydrnnndfxkz5kwx")))) + "1g8k90p0sbcb3rdrbldj5bcjp2piy5ldni4jplyr78vjpmrmvqk7")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9329,14 +9413,14 @@ datasets.") (define-public r-annotatr (package (name "r-annotatr") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "annotatr" version)) (sha256 (base32 - "0pcf4jrq05bmfxph41hmdx1x147k1ay5fl2h488y1s4h8qm3c67p")))) + "1ls1qdfppcxysggi3bghrnspb5a3s40pm2mj4x0whc7c40cf90mg")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9370,14 +9454,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.6.3") + (version "2.6.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "04nz85vr184fjmf2k0kc5sy2hjzpfazfkxlhlgax50rnkn98va5x")))) + "043m4512q73x6q529hqfgrap0fq5anvny4va085nafia06b805pi")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -9932,14 +10016,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.16.1") + (version "6.16.3") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0fiwf86hvkidxwkdcw0x7lk3bk2fsxqng43b1js7klifm3gfcf91")))) + "1x6dbw4q6p9vngm256fr96r9fjxk5nik5ivkhbl5a9zqyq8wagpa")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -10319,14 +10403,14 @@ regulatory networks from expression data.") (define-public r-roc (package (name "r-roc") - (version "1.68.0") + (version "1.68.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ROC" version)) (sha256 (base32 - "0ff5rcpyybgjzsfbhaslim0m02n3bksv1r9v7bq0gg0iyzll0rjc")))) + "1rmsrvn6hrg9ay7xfb05mfkxknnig78p3kbk9ghsd11lhx2fjm3s")))) (properties `((upstream-name . "ROC"))) (build-system r-build-system) (propagated-inputs @@ -10877,14 +10961,14 @@ 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 +11927,14 @@ 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 +12553,14 @@ 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 +12788,14 @@ 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 +12906,14 @@ 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 +12934,14 @@ 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) @@ -13010,14 +13094,14 @@ relevant, and the minimum expression of the most abundant condition.") (define-public r-catalyst (package (name "r-catalyst") - (version "1.16.1") + (version "1.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "CATALYST" version)) (sha256 (base32 - "12frw4myqr8y3ff4n74ld4478ndpmfj5ynr6gnigbr1h61b94m3v")))) + "1vw8x54hwgcyn29k81zcvawawy2iy2qgp49gjpb830q04gx6yc6h")))) (properties `((upstream-name . "CATALYST"))) (build-system r-build-system) (propagated-inputs @@ -13386,14 +13470,14 @@ functionalities including parsing, graph operation, visualization and etc.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "075jncvfbn3lydg0jvfhnv5025mnw79saa0k557vpcwdvs9y4p0c")))) + "16vp5psmigxdkkd6fbivb6s8mvd7rsnm771wsbjvayl2y7ig7kq4")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -13661,3 +13745,951 @@ starting site, start codon, stop codon and transcription ending site.") "This package provides flexible, quantitative, and integrative genomic 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 . 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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-beclear + (package + (name "r-beclear") + (version "2.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BEclear" version)) + (sha256 + (base32 + "0w18livng2gcmjgvws7pix3gsnj237rs34sgwxsfmn8p5vfx8b30")))) + (properties `((upstream-name . 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These sequences are generated based on expression of +all RNA-Seq libraries of each species integrated in Bgee.") + (license license:gpl3))) + +(define-public r-bgeedb + (package + (name "r-bgeedb") + (version "2.18.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BgeeDB" version)) + (sha256 + (base32 + "1ziq180yfpdqwhjdzkwjjhwzn3kb0gkj6q0a26c7a30mcfb50w11")))) + (properties `((upstream-name . 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This aims to provide a consistent +Python environment that can be used reliably by Bioconductor packages. +Functions are also provided to enable smooth interoperability of multiple +Python environments in a single R session.") + (license license:gpl3))) + +(define-public r-biocthis + (package + (name "r-biocthis") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biocthis" version)) + (sha256 + (base32 + "08awghsg7q22csb0j9dr8dpb1vkn9gcs9qnhhljxifkw2ahbqia4")))) + (properties `((upstream-name . 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Its architecture as a development framework facilitates +the development of new database connectors for local projects or inside +separate published packages.") + (license license:agpl3+))) + +(define-public r-biomformat + (package + (name "r-biomformat") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biomformat" version)) + (sha256 + (base32 + "1wgshkddxbmpsihpkm0dp7vqp59ns6iqbx574y80n2pxb8dx8sy9")))) + (properties `((upstream-name . "biomformat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-jsonlite" ,r-jsonlite) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-rhdf5" ,r-rhdf5))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/joey711/biomformat/") + (synopsis "Interface package for the BIOM file format") + (description + "This is an R package for interfacing with the BIOM format. This package +includes basic tools for reading biom-format files, accessing and subsetting +data tables from a biom object (which is more complex than a single table), as +well as limited support for writing a biom-object back to a biom-format file. +The design of this API is intended to match the Python API and other tools +included with the biom-format project, but with a decidedly \"R flavor\" that +should be familiar to R users. This includes S4 classes and methods, as well +as extensions of common core functions/methods.") + (license license:gpl2))) + +(define-public r-mvcclass + (package + (name "r-mvcclass") + (version "1.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MVCClass" version)) + (sha256 + (base32 + "1di7y10mr7caacd6igwxnr62cm4v1x877yi4a2i5jqz1058jqni7")))) + (properties `((upstream-name . 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BioNERO can be used +to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) +from gene expression data. Additionally, it can be used to explore +topological properties of protein-protein interaction (PPI) networks. GCN +inference relies on the popular WGCNA algorithm. GRN inference is based on +the \"wisdom of the crowds\" principle, which consists in inferring GRNs with +multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average +rank for each interaction pair. As all steps of network analyses are included +in this package, BioNERO makes users avoid having to learn the syntaxes of +several packages and how to communicate between them. Finally, users can also +identify consensus modules across independent expression sets and calculate +intra and interspecies module preservation statistics between different +networks.") + (license license:gpl3))) + +(define-public r-bionet + (package + (name "r-bionet") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNet" version)) + (sha256 + (base32 + "15rk1jfv4h1mxvr5bs0qmq6fdnza7zcmksigqxb46fs7f6znr3yi")))) + (properties `((upstream-name . 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By fitting a beta-uniform mixture model and +calculating scores from the p-values, overall scores of network regions can be +calculated and an integer linear programming algorithm identifies the maximum +scoring subnetwork.") + (license license:gpl2+))) + +(define-public r-bionetstat + (package + (name "r-bionetstat") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioNetStat" version)) + (sha256 + (base32 + "16xlfng9m8xvm831c2x6zmjc0gavlfiy9pnza55hdv86888fcnbg")))) + (properties `((upstream-name . "BioNetStat"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocparallel" ,r-biocparallel) + ("r-dt" ,r-dt) + ("r-ggplot2" ,r-ggplot2) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-knitr" ,r-knitr) + ("r-markdown" ,r-markdown) + ("r-pathview" ,r-pathview) + ("r-pheatmap" ,r-pheatmap) + ("r-plyr" ,r-plyr) + ("r-psych" ,r-psych) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rjsonio" ,r-rjsonio) + ("r-rmarkdown" ,r-rmarkdown) + ("r-shiny" ,r-shiny) + ("r-shinybs" ,r-shinybs) + ("r-whisker" ,r-whisker) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jardimViniciusC/BioNetStat") + (synopsis "Biological network analysis") + (description + "This package provides a package to perform differential network +analysis, differential node analysis (differential coexpression analysis), +network and metabolic pathways view.") + (license license:gpl3+))) + +(define-public r-bioqc + (package + (name "r-bioqc") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioQC" version)) + (sha256 + (base32 + "04akp94p0d0zid55m1b1k3qlw7iq914pcg57lihgj3pa92n1sc5l")))) + (properties `((upstream-name . "BioQC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-edger" ,r-edger) + ("r-rcpp" ,r-rcpp))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://accio.github.io/BioQC/") + (synopsis "Detect tissue heterogeneity in expression profiles with gene sets") + (description + "BioQC performs quality control of high-throughput expression data based +on tissue gene signatures. It can detect tissue heterogeneity in gene +expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is +optimised for high performance.") + (license license:gpl3+))) + +(define-public r-biotip + (package + (name "r-biotip") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BioTIP" version)) + (sha256 + (base32 + "1i6r8px0fmdjx8frpljppwql74mhx08ibvhs9y3qk91ck5h3f0js")))) + (properties `((upstream-name . "BioTIP"))) + (build-system r-build-system) + (propagated-inputs + `(("r-cluster" ,r-cluster) + ("r-genomicranges" ,r-genomicranges) + ("r-hmisc" ,r-hmisc) + ("r-igraph" ,r-igraph) + ("r-mass" ,r-mass) + ("r-psych" ,r-psych) + ("r-stringr" ,r-stringr))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/xyang2uchicago/BioTIP") + (synopsis "R package for characterization of biological tipping-point") + (description + "This package adopts tipping-point theory to transcriptome profiles to +help unravel disease regulatory trajectory.") + (license license:gpl2))) + +(define-public r-biotmle + (package + (name "r-biotmle") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biotmle" version)) + (sha256 + (base32 + "01smkmbv40yprgrgi2gjnmi8ncqyrlkfdxsh33ki20amcx32nc7f")))) + (properties `((upstream-name . "biotmle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-dofuture" ,r-dofuture) + ("r-dplyr" ,r-dplyr) + ("r-drtmle" ,r-drtmle) + ("r-future" ,r-future) + ("r-ggplot2" ,r-ggplot2) + ("r-ggsci" ,r-ggsci) + ("r-limma" ,r-limma) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-superheat" ,r-superheat) + ("r-tibble" ,r-tibble))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://code.nimahejazi.org/biotmle/") + (synopsis "Targeted learning with moderated statistics for biomarker discovery") + (description + "This package provides tools for differential expression biomarker +discovery based on microarray and next-generation sequencing data that +leverage efficient semiparametric estimators of the average treatment effect +for variable importance analysis. Estimation and inference of the (marginal) +average treatment effects of potential biomarkers are computed by targeted +minimum loss-based estimation, with joint, stable inference constructed across +all biomarkers using a generalization of moderated statistics for use with the +estimated efficient influence function. The procedure accommodates the use of +ensemble machine learning for the estimation of nuisance functions.") + (license license:expat))) + +(define-public r-bsseq + (package + (name "r-bsseq") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bsseq" version)) + (sha256 + (base32 + "1xpv85hr681kkkilsnasndkszwmzbzq11y0lff4na2ilsm7sqmmi")))) + (properties `((upstream-name . "bsseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-hdf5array" ,r-hdf5array) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-permute" ,r-permute) + ("r-r-utils" ,r-r-utils) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5" ,r-rhdf5) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/hansenlab/bsseq") + (synopsis "Analyze, manage and store bisulfite sequencing data") + (description + "This package provides a collection of tools for analyzing and +visualizing bisulfite sequencing data.") + (license license:artistic2.0))) + +(define-public r-dmrseq + (package + (name "r-dmrseq") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "dmrseq" version)) + (sha256 + (base32 + "1jbbjifjsnk9261wqmdwkbzj1w52g6vaanpk4w816ri0fap587m4")))) + (properties `((upstream-name . "dmrseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationhub" ,r-annotationhub) + ("r-annotatr" ,r-annotatr) + ("r-biocparallel" ,r-biocparallel) + ("r-bsseq" ,r-bsseq) + ("r-bumphunter" ,r-bumphunter) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-matrixstats" ,r-matrixstats) + ("r-nlme" ,r-nlme) + ("r-outliers" ,r-outliers) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/dmrseq") + (synopsis "Detection and inference of differentially methylated regions") + (description + "This package implements an approach for scanning the genome to detect +and perform accurate inference on differentially methylated regions from Whole +Genome Bisulfite Sequencing data. The method is based on comparing detected +regions to a pooled null distribution, that can be implemented even when as +few as two samples per population are available. Region-level statistics are +obtained by fitting a @dfn{generalized least squares} (GLS) regression model +with a nested autoregressive correlated error structure for the effect of +interest on transformed methylation proportions.") + (license license:expat))) + +(define-public r-biscuiteer + (package + (name "r-biscuiteer") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "biscuiteer" version)) + (sha256 + (base32 + "0f4kk4v2c5diq0fbvyvgwjd1kjk9izr6n9wfrlrr7wbx4pz3c3h6")))) + (properties `((upstream-name . "biscuiteer"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biscuiteerdata" ,r-biscuiteerdata) + ("r-bsseq" ,r-bsseq) + ("r-data-table" ,r-data-table) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dmrseq" ,r-dmrseq) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-gtools" ,r-gtools) + ("r-hdf5array" ,r-hdf5array) + ("r-homo-sapiens" ,r-homo-sapiens) + ("r-impute" ,r-impute) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-mus-musculus" ,r-mus-musculus) + ("r-qdnaseq" ,r-qdnaseq) + ("r-qualv" ,r-qualv) + ("r-r-utils" ,r-r-utils) + ("r-readr" ,r-readr) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/trichelab/biscuiteer") + (synopsis "Convenience functions for the Biscuit package") + (description + "This package provides a test harness for bsseq loading of Biscuit +output, summarization of WGBS data over defined regions and in mappable +samples, with or without imputation, dropping of mostly-NA rows, age +estimates, etc.") + (license license:gpl3))) + +(define-public r-tximeta + (package + (name "r-tximeta") + (version "1.10.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "tximeta" version)) + (sha256 + (base32 + "0ipgpcl93cac4qff6lp9x2l3gav5kb1x1d56g32h09hlm797rvvh")))) + (properties `((upstream-name . "tximeta"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-annotationhub" ,r-annotationhub) + ("r-biocfilecache" ,r-biocfilecache) + ("r-biostrings" ,r-biostrings) + ("r-ensembldb" ,r-ensembldb) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-jsonlite" ,r-jsonlite) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tibble" ,r-tibble) + ("r-tximport" ,r-tximport))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/mikelove/tximeta") + (synopsis "Transcript quantification import with automatic metadata") + (description + "This package implements transcript quantification import from Salmon and +alevin with automatic attachment of transcript ranges and release information, +and other associated metadata. De novo transcriptomes can be linked to the +appropriate sources with linkedTxomes and shared for computational +reproducibility.") + (license license:gpl2))) |