diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 354 |
1 files changed, 313 insertions, 41 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..31484799b2 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,112 @@ using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-amountain + (package + (name "r-amountain") + (version "1.22.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AMOUNTAIN" version)) + (sha256 + (base32 + "0vdfabsrisdd7qq28f5ivd0v8zz49szqn677i5lhwnlaix220c54")))) + (properties `((upstream-name . "AMOUNTAIN"))) + (build-system r-build-system) + (inputs (list gsl)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AMOUNTAIN") + (synopsis "Modules for multilayer weighted gene co-expression networks") + (description + "This package provides a pure data-driven gene network, @dfn{WGCN}(weighted +gene co-expression network) could be constructed only from expression profile. +Different layers in such networks may represent different time points, multiple +conditions or various species. @code{AMOUNTAIN} aims to search active modules +in multi-layer WGCN using a continuous optimization approach.") + (license license:gpl2+))) + +(define-public r-amaretto + (package + (name "r-amaretto") + (version "1.12.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AMARETTO" version)) + (sha256 + (base32 + "111dk19b9910icksyr592cvhc5gwvgknr5q4887j9yxbajd7hcmx")))) + (properties `((upstream-name . "AMARETTO"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocfilecache + r-callr + r-circlize + r-complexheatmap + r-curatedtcgadata + r-doparallel + r-dplyr + r-dt + r-foreach + r-ggplot2 + r-glmnet + r-gridextra + r-httr + r-impute + r-knitr + r-limma + r-matrix + r-matrixstats + r-multiassayexperiment + r-rcpp + r-readr + r-reshape2 + r-rmarkdown + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AMARETTO") + (synopsis "Regulatory network inference and driver gene evaluation") + (description + "This package @code{AMARETTO} represents an algorithm that integrates copy +number, DNA methylation and gene expression data to identify a set of driver +genes by analyzing cancer samples and connects them to clusters of co-expressed +genes, which we define as modules. @code{AMARETTO} can be applied in a pancancer +setting to identify cancer driver genes and their modules on multiple cancer +sites. @code{AMARETTO} captures modules enriched in angiogenesis, cell cycle +and EMT, and modules that accurately predict survival and molecular subtypes. +This allows @code{AMARETTO} to identify novel cancer driver genes directing +canonical cancer pathways.") + (license license:asl2.0))) + +(define-public r-anaquin + (package + (name "r-anaquin") + (version "2.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Anaquin" version)) + (sha256 + (base32 + "1jgpnls2djl1yzvnk64qc83mljmlci7wflwkza3wr0sv6r47b0dd")))) + (properties `((upstream-name . "Anaquin"))) + (build-system r-build-system) + (propagated-inputs + (list r-deseq2 + r-ggplot2 + r-knitr + r-locfit + r-plyr + r-qvalue + r-rocr)) + (native-inputs (list r-knitr)) + (home-page "https://www.sequinstandards.com/") + (synopsis "Statistical analysis of sequins") + (description + "The project is intended to support the use of @dfn{sequins}(synthetic +sequencing spike-in controls) owned and made available by the Garvan Institute +of Medical Research. The goal is to provide a standard open source library for +quantitative analysis, modelling and visualization of spike-in controls.") + (license license:bsd-3))) + (define-public r-aneufinder (package (name "r-aneufinder") @@ -2029,6 +2135,94 @@ calling, plotting, export and analysis from whole-genome single cell sequencing data.") (license license:artistic2.0))) +(define-public r-anf + (package + (name "r-anf") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ANF" version)) + (sha256 + (base32 + "1fa2pbdapymrpz01ws0m2fbzf11d723x6rbsys29v06is57f5lpj")))) + (properties `((upstream-name . "ANF"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-igraph + r-mass + r-rcolorbrewer + r-survival)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/ANF") + (synopsis "Affinity network fusion for complex patient clustering") + (description + "The package @dfn{ANF}(Affinity Network Fusion) provides methods for affinity +matrix construction and fusion as well as spectral clustering. This package is +used for complex patient clustering by integrating multi-omic data through affinity +network fusion.") + (license license:gpl3))) + +(define-public r-annmap + (package + (name "r-annmap") + (version "1.38.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "annmap" version)) + (sha256 + (base32 + "0ywqbb8jia7rrkzcsf6a11kqf8dnx96z8n8xw7067mahycykbixv")))) + (properties `((upstream-name . "annmap"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-dbi + r-digest + r-genefilter + r-genomicranges + r-iranges + r-lattice + r-rmysql + r-rsamtools)) + (home-page "https://github.com/cruk-mi/annmap") + (synopsis + "Genome annotation and visualisation for Affymetrix arrays and NGS analysis") + (description + "This package @code{annmap} provides annotation mappings for Affymetrix exon +arrays and coordinate based queries to support deep sequencing data analysis. +Database access is hidden behind the API which provides a set of functions such +as @code{genesInRange()}, @code{geneToExon()}, @code{exonDetails()}, etc. +Functions to plot gene architecture and BAM file data are also provided.") + (license license:gpl2))) + +(define-public r-antiprofiles + (package + (name "r-antiprofiles") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "antiProfiles" version)) + (sha256 + (base32 + "1277kg5xpyb2yriyjy18p437q5lj22h4al7z7pygkzxzywxv9g40")))) + (properties `((upstream-name . "antiProfiles"))) + (build-system r-build-system) + (propagated-inputs + (list r-locfit + r-matrixstats)) + (home-page "https://github.com/HCBravoLab/antiProfiles") + (synopsis "Implementation of gene expression anti-profiles") + (description + "This package implements the gene expression anti-profiles method. +Anti-profiles are a new approach for developing cancer genomic signatures that +specifically take advantage of gene expression heterogeneity. They explicitly +model increased gene expression variability in cancer to define robust and +reproducible gene expression signatures capable of accurately distinguishing +tumor samples from healthy controls.") + (license license:artistic2.0))) + (define-public r-biocversion (package (name "r-biocversion") @@ -2746,6 +2940,25 @@ measures for Affymetrix Oligonucleotide Arrays.") (properties `((upstream-name . "AffyCompatible"))) (build-system r-build-system) + (arguments + (list + #:phases + `(modify-phases %standard-phases + (add-after 'unpack 'make-reproducible + (lambda _ + ;; Order DTD elements before generating R code from them. + (substitute* "R/methods-AffyCompatible.R" + (("dtd <- .*" m) + (string-append m " +elements <- dtd$elements +ordered <- elements[order(names(elements))]\n")) + (("elt in dtd\\$elements") + "elt in ordered")) + ;; Use a predictable directory name for code generation. + (mkdir-p "/tmp/NetAffxResourcePrototype") + (substitute* "R/DataClasses.R" + (("directory=tempdir\\(\\)") + "directory=\"/tmp/NetAffxResourcePrototype\""))))))) (propagated-inputs (list r-biostrings r-rcurl r-xml)) (home-page "https://bioconductor.org/packages/AffyCompatible/") @@ -3660,6 +3873,50 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.") (license license:lgpl3))) +(define-public r-dittoseq + (package + (name "r-dittoseq") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "dittoSeq" version)) + (sha256 + (base32 + "0vi0hcyffaxp6yxsrq95bdlrhr85dvbqm9c7rg6a6blkfgwhlzb4")))) + (properties `((upstream-name . "dittoSeq"))) + (build-system r-build-system) + (propagated-inputs + (list r-colorspace + r-cowplot + r-ggplot2 + r-ggrepel + r-ggridges + r-gridextra + r-pheatmap + r-reshape2 + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/dittoSeq") + (synopsis "Single-cell and bulk RNA sequencing visualization") + (description + "This package provides a universal, user friendly, single-cell and bulk RNA +sequencing visualization toolkit that allows highly customizable creation of +color blindness friendly, publication-quality figures. dittoSeq accepts both +SingleCellExperiment (SCE) and Seurat objects, as well as the import and +usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. +Visualizations include dimensionality reduction plots, heatmaps, scatterplots, +percent composition or expression across groups, and more. Customizations +range from size and title adjustments to automatic generation of annotations +for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton +plot, hidden data overlay upon cursor hovering via ggplotly conversion, and +many more. All with simple, discrete inputs. Color blindness friendliness is +powered by legend adjustments (enlarged keys), and by allowing the use of +shapes or letter-overlay in addition to the carefully selected +code{dittoColors()}.") + (license license:expat))) + (define-public r-edaseq (package (name "r-edaseq") @@ -3728,14 +3985,14 @@ CAGE.") (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.20.1") + (version "2.20.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "183rs74ngfvn9xz36csch495pqaash90yhhikm73m7b2bc37ziwz")))) + "12n21dcimdhgyjzk33m6xbv0m9ihgyzcf66vr1jr5ycv3rq2s7xc")))) (build-system r-build-system) (propagated-inputs (list r-annotationdbi @@ -4282,13 +4539,13 @@ Binomial data via estimation of latent structure in the natural parameter.") (define-public r-limma (package (name "r-limma") - (version "3.52.1") + (version "3.52.2") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "193l3z2jv0kr91nl4r64p3jzb2rai9k8akx1zw7303nsnwpiiaay")))) + "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -4605,14 +4862,14 @@ previously been used in XCMS.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.38.0") + (version "1.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "1xklaiyd4mv9sf9211flq1s68fhdn53y2i4l1k2ib39a4l6y9cyr")))) + "0mxnxj8x4hc21psz39mf7qwvh1fsn6qyjgl5qffk1xxmasf69619")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -4976,14 +5233,14 @@ tab-delimited (tabix) files.") (define-public r-restfulr (package (name "r-restfulr") - (version "0.0.14") + (version "0.0.15") (source (origin (method url-fetch) (uri (cran-uri "restfulr" version)) (sha256 (base32 - "1sdlz8zl4xvd7cpn1gm86q7jv9v7561gg4wk6y7zybiw37pxghq6")))) + "14p6h0gjknqy5z2fprxw7waf4p0cd2qmp18s7qig4ylqn8gqzzs0")))) (properties `((upstream-name . "restfulr"))) (build-system r-build-system) (propagated-inputs @@ -4997,13 +5254,13 @@ tab-delimited (tabix) files.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.56.0") + (version "1.56.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1d9sak1xrrkcvj0q3vnp6w2k0nx2k2ajhsbq0dyb4nhcghp5w8fd")))) + "10qy9s6253mgj871qfqn03i8yw10mz7id4cxfyf67qxczz2xmjls")))) (build-system r-build-system) (arguments `(#:phases @@ -5289,14 +5546,14 @@ ungapped alignment formats.") (define-public r-simplifyenrichment (package (name "r-simplifyenrichment") - (version "1.6.0") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "simplifyEnrichment" version)) (sha256 (base32 - "1g3kfa17p60jkk4l34vc5hdq83w082qsxbjvpqw7r9rdd8d79z2q")))) + "0qblgdxmr7zc981529cca3ykakql618q1im6gaxw8pwws5jgpyk6")))) (properties `((upstream-name . "simplifyEnrichment"))) (build-system r-build-system) @@ -5953,13 +6210,13 @@ libraries for systems that do not have these available via other means.") (define-public r-zellkonverter (package (name "r-zellkonverter") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "zellkonverter" version)) (sha256 - (base32 "0s1n3impm4k55pac8mr18czylsc30yqcvdfdki4sawk74b2rkx8c")))) + (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz")))) (properties `((upstream-name . "zellkonverter"))) (build-system r-build-system) (propagated-inputs @@ -6481,13 +6738,13 @@ enrichedGO (addGeneIDs).") (define-public r-matrixgenerics (package (name "r-matrixgenerics") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MatrixGenerics" version)) (sha256 (base32 - "0s7s39v9lqniirjgp8lbmffw0c8rsp6bndgzy1zlyh5vivfih0f5")))) + "1liblnpziyyjxzrhdd5d89ilvfqqhbl87h3hsmdm0kwnmc73r37f")))) (properties `((upstream-name . "MatrixGenerics"))) (build-system r-build-system) @@ -7618,14 +7875,14 @@ multiplication and calculation of row/column sums or means.") (define-public r-batchelor (package (name "r-batchelor") - (version "1.12.1") + (version "1.12.3") (source (origin (method url-fetch) (uri (bioconductor-uri "batchelor" version)) (sha256 (base32 - "1zyvjr9nwfh0cdqk4kwmr30yhh05picyab1hpnpn737xvn525jfi")))) + "00ix3hvhgalxg63qnynv2waa273jk336lg47k72qwxfzimsxfjxc")))) (properties `((upstream-name . "batchelor"))) (build-system r-build-system) (propagated-inputs @@ -8368,17 +8625,22 @@ are standardized and usable by the accompanying mutossGUI package.") (define-public r-metap (package (name "r-metap") - (version "1.3") + (version "1.8") (source (origin (method url-fetch) (uri (cran-uri "metap" version)) (sha256 (base32 - "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) + "0asmypxfxly4xmcjf3yzid5zqlzg88z0brij2splfk4avsl035gf")))) (build-system r-build-system) (propagated-inputs - (list r-lattice r-mutoss r-rdpack r-tfisher)) + (list r-lattice + r-mathjaxr + r-mutoss + r-qqconf + r-rdpack + r-tfisher)) (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") (synopsis "Meta-analysis of significance values") (description @@ -8743,14 +9005,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.4.2") + (version "4.4.4") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "07fbc3d06990qy1qcaqqgm5ma2l0h08bwfkqrnlfd9f2xcppdywd")))) + "0k5jhry0j6wa7779n3hrw4ld4bvyahpgpbwi2a0g704m3dd3mqp5")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -9290,14 +9552,14 @@ type and symbol colors.") (define-public r-genomicscores (package (name "r-genomicscores") - (version "2.8.0") + (version "2.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicScores" version)) (sha256 (base32 - "0zq9k4189dlc14f9rknsc1ffhpjzb2f4fzdaszfdbnd4rr43b79i")))) + "12rcxw69an1d5q7ar58xy8s871l47imw2nm08j054ivxslx8597j")))) (properties `((upstream-name . "GenomicScores"))) (build-system r-build-system) (propagated-inputs @@ -9311,6 +9573,7 @@ type and symbol colors.") r-genomeinfodb r-genomicranges r-hdf5array + r-httr r-iranges r-rhdf5 r-s4vectors @@ -10705,17 +10968,20 @@ packages.") (define-public r-ropls (package (name "r-ropls") - (version "1.28.0") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ropls" version)) (sha256 (base32 - "1i9g32mjknrd2lbz2nisc7nr0gk9byx9aik1i7xdwmq4ndxf8rf7")))) + "07gpx15r8c3wljiwxnff2zp7wxbhzz9r7njk8zg8hpy2q5qm3i6c")))) (build-system r-build-system) (propagated-inputs - (list r-biobase r-multidataset)) + (list r-biobase + r-multiassayexperiment + r-multidataset + r-summarizedexperiment)) (native-inputs (list r-knitr)) ; for vignettes (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") @@ -10742,17 +11008,23 @@ coefficients).") (define-public r-biosigner (package (name "r-biosigner") - (version "1.24.0") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biosigner" version)) (sha256 (base32 - "11w28nlz0f06idbna5k9xs891w516401l1zab5gg7s0z3xxaki4f")))) + "0vdv2by3qv7y8vzr8qgg7apwwgsa0fhlfrhzns7g3nas7883c89m")))) (build-system r-build-system) (propagated-inputs - (list r-biobase r-e1071 r-multidataset r-randomforest r-ropls)) + (list r-biobase + r-e1071 + r-multiassayexperiment + r-multidataset + r-randomforest + r-ropls + r-summarizedexperiment)) (native-inputs (list r-knitr)) (home-page "https://bioconductor.org/packages/biosigner/") @@ -10812,14 +11084,14 @@ annotations.") (define-public r-rsubread (package (name "r-rsubread") - (version "2.10.2") + (version "2.10.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsubread" version)) (sha256 (base32 - "1pvyx8nxv10s816hgxrnw60hp9rlqjdgjq3ajpzqxgxmmlhnk0v0")))) + "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl")))) (properties `((upstream-name . "Rsubread"))) (build-system r-build-system) (inputs (list zlib)) @@ -14679,14 +14951,14 @@ by Ernst and Kellis.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.44.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1lvms07ba99nzf10gpn50wjca84nj5jrb6902z069p2bfi4xyd27")))) + "0iyhjalwq1jmldpn20iv8l2kmz6sm20ddry2yz2zn7yq0wszp3vg")))) (build-system r-build-system) (arguments `(#:phases @@ -15363,14 +15635,14 @@ all RNA-Seq libraries of each species integrated in Bgee.") (define-public r-bgeedb (package (name "r-bgeedb") - (version "2.22.0") + (version "2.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "BgeeDB" version)) (sha256 (base32 - "093zk43x8i9ajaqsdhndkyal3dizllr3g85ziavb3k73dzvarzsc")))) + "1f6lrazaibbz21sqvj59rq6ps9m1riw2y0kyidbn29mxf4ibwh3k")))) (properties `((upstream-name . "BgeeDB"))) (build-system r-build-system) (propagated-inputs @@ -15832,14 +16104,14 @@ scoring subnetwork.") (define-public r-bionetstat (package (name "r-bionetstat") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BioNetStat" version)) (sha256 (base32 - "0f387j35lj32ryiw48jz8gc08al2lmmv9zvbbgyjq9wmqlca3dfb")))) + "0zs6pymvxb95sji0rnnzaz3whj7hsvj2kl4n4gzj7w1q0prbfpb2")))) (properties `((upstream-name . "BioNetStat"))) (build-system r-build-system) (propagated-inputs @@ -16169,13 +16441,13 @@ estimates, etc.") (define-public r-tcgabiolinks (package (name "r-tcgabiolinks") - (version "2.24.1") + (version "2.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "TCGAbiolinks" version)) (sha256 - (base32 "0kw4lrg8xm0ipj7f7h1rwfj7a8mknkril1pn05x08mx13f7p5p14")))) + (base32 "0visvfhzaf0p1rb5vjkmw1c91zfxpks8nl9nbl9xlnpm8lkmmkms")))) (properties `((upstream-name . "TCGAbiolinks"))) (build-system r-build-system) (propagated-inputs |