diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 284 |
1 files changed, 269 insertions, 15 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 5d29a3acf2..a25f56ad02 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -11,6 +11,7 @@ ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> +;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -286,6 +287,28 @@ RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") (license license:artistic2.0))) +(define-public r-bsgenome-drerio-ucsc-danrer11 + (package + (name "r-bsgenome-drerio-ucsc-danrer11") + (version "1.4.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Drerio.UCSC.danRer11" + version 'annotation)) + (sha256 + (base32 "08a928mqzv2jxngjcs4yr6ni1b9z9al6jdngwi438j8hm41cwk4v")))) + (properties `((upstream-name . "BSgenome.Drerio.UCSC.danRer11"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bsgenome" ,r-bsgenome))) + (home-page "https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11") + (synopsis "Full genome sequences for Danio rerio (UCSC version danRer11)") + (description + "This package provides full genome sequences for Danio rerio (Zebrafish) +as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (package (name "r-bsgenome-hsapiens-1000genomes-hs37d5") @@ -1588,6 +1611,33 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), @code{Matrix} objects, and ordinary arrays and data frames.") (license license:artistic2.0))) +(define-public r-derfinderhelper + (package + (name "r-derfinderhelper") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "derfinderHelper" version)) + (sha256 + (base32 "06x0wy2wzpngak1pnrj2p0xzlx1nbcz0hs3p9q5ic6ib2rgwrh35")))) + (properties `((upstream-name . "derfinderHelper"))) + (build-system r-build-system) + (propagated-inputs + `(("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/leekgroup/derfinderHelper") + (synopsis "Helper for derfinder") + (description + "This package speeds up the derfinder package when using multiple cores. +It is particularly useful when using BiocParallel and it helps reduce the time +spent loading the full derfinder package when running the F-statistics +calculation in parallel.") + (license license:artistic2.0))) + (define-public r-bluster (package (name "r-bluster") @@ -2234,13 +2284,13 @@ on Bioconductor or which replace R functions.") (define-public r-biomart (package (name "r-biomart") - (version "2.50.0") + (version "2.50.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "069wqihm8pj3r41dizvdbj4jnw9bsc5jrz8czfrak5v69bgk5v5q")))) + "1lm8axjmi2k1d2x0gdlvs0fzsd68xvxx7sn1wn6v4wr0pv85qhkz")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -2272,13 +2322,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0jqgbpjppwinzw100qhc42kc95znq6xanl26bi8m9cq7yggbpra6")))) + "04s6y7q9dvg26fazs6lzkm668zpl3136j9gd5hkyihyrf4a1w3g3")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -3164,13 +3214,13 @@ provide added flexibility for data combination and manipulation.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.46.0") + (version "1.46.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "03fdmzcf8h17ksa3byc3k5mxc65pqrbcnw00myz1q53l01p3cnf2")))) + "133r27wsdyppjv9kq0d2xamx007lkf416nnlaygs4hs3a76p9xwx")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -4143,6 +4193,46 @@ differential expression analysis, RNAseq data and related problems.") ;; Any version of the LGPL (license license:lgpl3+))) +(define-public r-scdblfinder + (package + (name "r-scdblfinder") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scDblFinder" version)) + (sha256 + (base32 "0wzmmcsnjybgzbc5rn4i72n26j9n59dfy1zg8ij0q8p4276jplsd")))) + (properties `((upstream-name . "scDblFinder"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-bluster" ,r-bluster) + ("r-delayedarray" ,r-delayedarray) + ("r-igraph" ,r-igraph) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors) + ("r-scater" ,r-scater) + ("r-scran" ,r-scran) + ("r-scuttle" ,r-scuttle) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-xgboost" ,r-xgboost))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/plger/scDblFinder") + (synopsis "Detect multiplets in single-cell RNA sequencing data") + (description + "The scDblFinder package gathers various methods for the detection and +handling of doublets/multiplets in single-cell RNA sequencing data (i.e. +multiple cells captured within the same droplet or reaction volume). It +includes methods formerly found in the scran package, and the new fast and +comprehensive scDblFinder method.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") @@ -4337,6 +4427,39 @@ events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) +(define-public r-stringdb + (package + (name "r-stringdb") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "STRINGdb" version)) + (sha256 + (base32 "1hvb73anhbf1g82nn5m11s783z6ihvlavf7p30w29qggxggnl6lm")))) + (properties `((upstream-name . "STRINGdb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-gplots" ,r-gplots) + ("r-hash" ,r-hash) + ("r-igraph" ,r-igraph) + ("r-plotrix" ,r-plotrix) + ("r-plyr" ,r-plyr) + ("r-png" ,r-png) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rcurl" ,r-rcurl) + ("r-sqldf" ,r-sqldf))) + (home-page "https://git.bioconductor.org/packages/STRINGdb") + (synopsis "Search tool for the retrieval of interacting proteins database") + (description + "The @code{STRINGdb} package provides an R interface to the STRING +protein-protein interactions database. @url{https://www.string-db.org, +STRING} is a database of known and predicted protein-protein interactions. +The interactions include direct (physical) and indirect (functional) +associations. Each interaction is associated with a combined confidence score +that integrates the various evidences.") + (license license:gpl2))) + (define-public r-structuralvariantannotation (package (name "r-structuralvariantannotation") @@ -4613,6 +4736,69 @@ their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.") (license license:artistic2.0))) +(define-public r-xina + (package + (name "r-xina") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "XINA" version)) + (sha256 + (base32 "14j1rn3p7i0rlqkbbg0a6pyhb97ifzvsbw6vfxw9pna7zv7rbhsp")))) + (properties `((upstream-name . "XINA"))) + (build-system r-build-system) + (propagated-inputs + `(("r-alluvial" ,r-alluvial) + ("r-ggplot2" ,r-ggplot2) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-mclust" ,r-mclust) + ("r-plyr" ,r-plyr) + ("r-stringdb" ,r-stringdb))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://git.bioconductor.org/packages/XINA") + (synopsis "Identifying proteins that exhibit similar patterns") + (description + "The aim of @code{XINA} is to determine which proteins exhibit similar +patterns within and across experimental conditions, since proteins with +co-abundance patterns may have common molecular functions. @code{XINA} imports +multiple datasets, tags dataset in silico, and combines the data for subsequent +subgrouping into multiple clusters. The result is a single output depicting +the variation across all conditions. @code{XINA} not only extracts +coabundance profiles within and across experiments, but also incorporates +protein-protein interaction databases and integrative resources such as +@dfn{Kyoto encyclopedia of genes and genomes} (KEGG) to infer interactors and +molecular functions, respectively, and produces intuitive graphical outputs.") + (license license:gpl3))) + +(define-public r-xmapbridge + (package + (name "r-xmapbridge") + (version "1.52.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "xmapbridge" version)) + (sha256 + (base32 "1zsqhisbq6f9qgw9f0a6ixxh635h3qm17117yfns5nnfw73ndlgi")))) + (properties `((upstream-name . "xmapbridge"))) + (build-system r-build-system) + (home-page "https://git.bioconductor.org/packages/xmapbridge") + (synopsis "Display numeric data in the web based genome browser X:MAP") + (description + "The package @code{xmapbridge} can plot graphs in the X:Map genome +browser. X:Map uses the Google Maps API to provide a scrollable view of the +genome. It supports a number of species, and can be accessed at +@url{http://xmap.picr.man.ac.uk}. This package exports plotting files in a +suitable format. Graph plotting in R is done using calls to the functions +@code{xmap.plot} and @code{xmap.points}, which have parameters that aim to be +similar to those used by the standard plot methods in R. These result in data +being written to a set of files (in a specific directory structure) that +contain the data to be displayed, as well as some additional meta-data +describing each of the graphs.") + (license license:lgpl3))) + (define-public r-xvector (package (name "r-xvector") @@ -7420,14 +7606,14 @@ to multiple hypothesis correction.") (define-public r-dose (package (name "r-dose") - (version "3.20.0") + (version "3.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DOSE" version)) (sha256 (base32 - "0hj5hn54g8a3gj4q9200bffcy9m1mvkiwbg60ysv1hxxbpi57kmv")))) + "10kknaqz40pb6v0fcjzp12hfpi6k5kvlqnyxx1k3y0h0wdg8hs3n")))) (properties `((upstream-name . "DOSE"))) (build-system r-build-system) (propagated-inputs @@ -8791,14 +8977,14 @@ based on @dfn{Continuous Wavelet Transform} (CWT).") (define-public r-xcms (package (name "r-xcms") - (version "3.16.0") + (version "3.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "xcms" version)) (sha256 (base32 - "0m6w68ndf2a4k148pbb0bbbgq57akzqgi9nf7k6ngkk22j3m7m95")))) + "19kjyi6br9qp2pnp24shgbww3iqaaqxk9791w8w8qbd6sxijd143")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9837,7 +10023,6 @@ statistics to the plot.") ("r-flowviz" ,r-flowviz) ("r-graph" ,r-graph) ("r-mnormt" ,r-mnormt))) - #; (inputs `(("gsl" ,gsl))) (native-inputs @@ -10114,14 +10299,14 @@ self-organizing map clustering and minimal spanning trees.") (define-public r-mixomics (package (name "r-mixomics") - (version "6.18.0") + (version "6.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mixOmics" version)) (sha256 (base32 - "0jwkb5scc33nfn2mibga8vp00pmc24ham71gpkbizvy43cy85icf")))) + "1wpskrnl2bry9m4k2djhjddcd8gpwf51gp5c3si1y7qxja78ql9f")))) (properties `((upstream-name . "mixOmics"))) (build-system r-build-system) (propagated-inputs @@ -11523,6 +11708,37 @@ visualization functions for compound clustering results and chemical structures.") (license license:artistic2.0))) +(define-public r-fmcsr + (package + (name "r-fmcsr") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "fmcsR" version)) + (sha256 + (base32 "0mshslfj7jsix1yc03s54spbbi56zspic49kfsjfv8npikj1i5w0")))) + (properties `((upstream-name . "fmcsR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-chemminer" ,r-chemminer) + ("r-runit" ,r-runit))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/girke-lab/fmcsR") + (synopsis "Mismatch tolerant maximum common substructure searching") + (description + "The fmcsR package introduces an efficient @dfn{maximum common +substructure} (MCS) algorithms combined with a novel matching strategy that +allows for atom and/or bond mismatches in the substructures shared among two +small molecules. The resulting flexible MCSs (FMCSs) are often larger than +strict MCSs, resulting in the identification of more common features in their +source structures, as well as a higher sensitivity in finding compounds with +weak structural similarities. The fmcsR package provides several utilities to +use the FMCS algorithm for pairwise compound comparisons, structure similarity +searching and clustering.") + (license license:artistic2.0))) + (define-public r-bioassayr (package (name "r-bioassayr") @@ -12379,13 +12595,13 @@ routines.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.32.2") + (version "0.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0xrmii2dnwyknpjdiwwjlklgzpbk9q09br27rq5ffz08if9yyk20")))) + "0wp29v41f9cf6khq2ww0f63nsq6219l1ycajzdqp3a2xda734ncw")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -14882,3 +15098,41 @@ and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.") (license license:gpl2))) + +(define-public r-phyloseq + (package + (name "r-phyloseq") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "phyloseq" version)) + (sha256 + (base32 "0k0aj8f7g1vr7l0qcc507b3w67zc1k9x7sdblm7mjb20zqr3916s")))) + (properties `((upstream-name . "phyloseq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-ade4" ,r-ade4) + ("r-ape" ,r-ape) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomformat" ,r-biomformat) + ("r-biostrings" ,r-biostrings) + ("r-cluster" ,r-cluster) + ("r-data-table" ,r-data-table) + ("r-foreach" ,r-foreach) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-multtest" ,r-multtest) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-vegan" ,r-vegan))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/joey711/phyloseq") + (synopsis "Handling and analysis of high-throughput microbiome census data") + (description + "Phyloseq provides a set of classes and tools to facilitate the import, +storage, analysis, and graphical display of microbiome census data.") + (license license:agpl3))) |