diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 207 |
1 files changed, 202 insertions, 5 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 94c92abefa..facfb75abf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -35,6 +35,7 @@ #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) + #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) @@ -1220,6 +1221,27 @@ demonstration purposes in the @code{AneuFinder} package.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-bladderbatch + (package + (name "r-bladderbatch") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bladderbatch" version + 'experiment)) + (sha256 + (base32 + "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k")))) + (properties `((upstream-name . "bladderbatch"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/bladderbatch") + (synopsis "Bladder gene expression data illustrating batch effects") + (description + "This package contains microarray gene expression data on 57 bladder samples from +5 batches. The data are used as an illustrative example for the sva package.") + (license license:artistic2.0))) + (define-public r-biscuiteerdata (package (name "r-biscuiteerdata") @@ -1540,6 +1562,30 @@ harmonized subsetting of rows (features) and columns (patients / samples) across the entire multi-'omics experiment.") (license license:artistic2.0))) +(define-public r-parathyroidse + (package + (name "r-parathyroidse") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "parathyroidSE" version + 'experiment)) + (sha256 + (base32 + "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16")))) + (properties `((upstream-name . "parathyroidSE"))) + (build-system r-build-system) + (propagated-inputs (list r-summarizedexperiment)) + (home-page "https://bioconductor.org/packages/parathyroidSE") + (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors") + (description + "This package provides @code{RangedSummarizedExperiment} objects of read +counts in genes and exonic parts for paired-end RNA-Seq data from experiments on +primary cultures of parathyroid tumors. The sequencing was performed on tumor +cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).") + ;; The author(s) mentions only LGPL without any specific version. + (license license:lgpl2.1+))) + (define-public r-tcgabiolinksgui-data (package (name "r-tcgabiolinksgui-data") @@ -2090,8 +2136,8 @@ canonical cancer pathways.") (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.") +of Medical Research. The goal is to provide a standard library for quantitative +analysis, modelling, and visualization of spike-in controls.") (license license:bsd-3))) (define-public r-aneufinder @@ -5016,6 +5062,45 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) +(define-public r-organism-dplyr + (package + (name "r-organism-dplyr") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Organism.dplyr" version)) + (sha256 + (base32 + "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as")))) + (properties `((upstream-name . "Organism.dplyr"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-annotationfilter + r-biocfilecache + r-dbi + r-dbplyr + r-dplyr + r-genomeinfodb + r-genomicfeatures + r-genomicranges + r-iranges + r-rlang + r-rsqlite + r-s4vectors + r-tibble)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/Organism.dplyr") + (synopsis "Dplyr-based access to Bioconductor annotation resources") + (description + "This package provides an alternative interface to Bioconductor @code{ +annotation} resources, in particular the gene identifier mapping functionality +of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate +functionality of the @code{TxDb} packages (e.g., +@code{TxDb.Hsapiens.UCSC.hg38.knownGene}).") + (license license:artistic2.0))) + (define-public r-organismdbi (package (name "r-organismdbi") @@ -5048,6 +5133,61 @@ annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.") (license license:artistic2.0))) +(define-public r-pcaexplorer + (package + (name "r-pcaexplorer") + (version "2.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pcaExplorer" version)) + (sha256 + (base32 + "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl")))) + (properties `((upstream-name . "pcaExplorer"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-base64enc + r-biomart + r-deseq2 + r-dt + r-genefilter + r-genomicranges + r-ggplot2 + r-ggrepel + r-go-db + r-gostats + r-heatmaply + r-iranges + r-knitr + r-limma + r-nmf + r-pheatmap + r-plotly + r-plyr + r-rmarkdown + r-s4vectors + r-scales + r-shiny + r-shinyace + r-shinybs + r-shinydashboard + r-summarizedexperiment + r-threejs + r-tidyr + r-topgo)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/federicomarini/pcaExplorer") + (synopsis + "Interactive Visualization of RNA-seq Data Using a Principal Components Approach") + (description + "This package provides functionality for interactive visualization of RNA-seq +datasets based on Principal Components Analysis. The methods provided allow for +quick information extraction and effective data exploration. A Shiny +application encapsulates the whole analysis.") + (license license:expat))) + (define-public r-pcamethods (package (name "r-pcamethods") @@ -5611,6 +5751,38 @@ a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.") (license license:gpl3))) +(define-public r-scry + (package + (name "r-scry") + (version "1.8.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scry" version)) + (sha256 + (base32 + "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193")))) + (properties `((upstream-name . "scry"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocsingular + r-delayedarray + r-glmpca + r-hdf5array + r-matrix + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scry.html") + (synopsis "Small-count analysis methods for high-dimensional data") + (description + "Many modern biological datasets consist of small counts that are not +well fit by standard linear-Gaussian methods such as principal component +analysis. This package provides implementations of count-based feature +selection and dimension reduction algorithms. These methods can be used to +facilitate unsupervised analysis of any high-dimensional data such as +single-cell RNA-seq.") + (license license:artistic2.0))) + (define-public r-seqlogo (package (name "r-seqlogo") @@ -6541,9 +6713,10 @@ problems in genomics, brain imaging, astrophysics, and data mining.") `(("r-knitr" ,r-knitr))) (home-page "https://github.com/yixuan/RcppNumerical") (synopsis "Rcpp integration for numerical computing libraries") - (description "This package provides a collection of open source libraries -for numerical computing (numerical integration, optimization, etc.) and their -integration with @code{Rcpp}.") + (description + "This package provides a collection of libraries for numerical computing +(numerical integration, optimization, etc.) and their integration with +@code{Rcpp}.") (license license:gpl2+))) (define-public r-apeglm @@ -7917,6 +8090,16 @@ coordinates.") (base32 "0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g")))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'make-build-order-reproducible + (lambda _ + (substitute* '("src/SYMPHONY/Cgl/configure.ac" + "src/SYMPHONY/Cgl/configure") + (("for file in `ls \\*/Makefile.in`") + "for file in `ls */Makefile.in | sort`"))))))) (inputs (list zlib)) (native-inputs @@ -12985,8 +13168,22 @@ gene expression.") "0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk")))) (properties `((upstream-name . "bgx"))) (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'do-not-tune-cflags-for-reproducibility + (lambda _ + (substitute* "configure.ac" + (("AX_GCC_ARCHFLAG.*") "")) + (delete-file "configure") + (invoke "autoreconf" "-vif")))))) + (inputs + (list boost)) (propagated-inputs (list r-affy r-biobase r-gcrma r-rcpp)) + (native-inputs + (list autoconf automake)) (home-page "https://bioconductor.org/packages/bgx/") (synopsis "Bayesian gene expression") (description |