diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 150 |
1 files changed, 147 insertions, 3 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 316aa20026..a7af5c42ce 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> @@ -7324,13 +7324,13 @@ global-scaling and full-quantile normalization.") (define-public r-edger (package (name "r-edger") - (version "4.0.3") + (version "4.0.5") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0sz46pwa1bsqrff2igswfhhj1fcwzn34zrlawy4fnb58z48kccb0")))) + "16cghh83v14jdq5n6xkm3jxj87n6l6zrxjgqdwb2ffgc26vkpb7w")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7462,6 +7462,37 @@ chromosome region or transcript models of lincRNA genes.") ;; No version specified (license license:lgpl3+))) +(define-public r-epidish + (package + (name "r-epidish") + (version "2.18.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "EpiDISH" version)) + (sha256 + (base32 "170ym3y6gd1kxghz2g5ynvgi1wrxx87b568cjcvzidpqkrkg87s6")))) + (properties `((upstream-name . "EpiDISH"))) + (build-system r-build-system) + (propagated-inputs (list r-e1071 + r-locfdr + r-mass + r-matrix + r-matrixstats + r-quadprog + r-stringr)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/sjczheng/EpiDISH") + (synopsis "Epigenetic dissection of intra-sample-heterogeneity") + (description + "@code{EpiDISH} is a R package to infer the proportions of a priori known +cell-types present in a sample representing a mixture of such cell-types. +Right now, the package can be used on DNAm data of whole blood, generic +epithelial tissue and breast tissue. Besides, the package provides a function +that allows the identification of differentially methylated cell-types and +their directionality of change in Epigenome-Wide Association Studies.") + (license license:gpl2))) + (define-public r-fastseg (package (name "r-fastseg") @@ -10315,6 +10346,49 @@ comprehensive scDblFinder method.") (license license:gpl3))) ;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scgate + (package + (name "r-scgate") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "scGate" version)) + (sha256 + (base32 "0h12d36zjc6fvxbhkxrzbpvw49z9fgyn1jc941q70ajw1yqi2hhh")))) + (properties `((upstream-name . "scGate"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-dplyr + r-ggplot2 + r-ggridges + r-patchwork + r-reshape2 + r-seurat + r-ucell)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/carmonalab/scGate") + (synopsis + "Marker-based cell type purification for single-cell sequencing data") + (description + "This package provides a method to purify a cell type or cell population +of interest from heterogeneous datasets. scGate package automatizes +marker-based purification of specific cell populations, without requiring +training data or reference gene expression profiles. scGate takes as input a +gene expression matrix stored in a Seurat object and a @acronym{GM, gating +model}, consisting of a set of marker genes that define the cell population of +interest. It evaluates the strength of signature marker expression in each +cell using the rank-based method UCell, and then performs @acronym{kNN, +k-nearest neighbor} smoothing by calculating the mean UCell score across +neighboring cells. kNN-smoothing aims at compensating for the large degree of +sparsity in scRNAseq data. Finally, a universal threshold over kNN-smoothed +signature scores is applied in binary decision trees generated from the +user-provided gating model, to annotate cells as either “pure” or “impure”, +with respect to the cell population of interest.") + (license license:gpl3))) + +;; This is a CRAN package, but it depends on packages from Bioconductor. (define-public r-scistreer (package (name "r-scistreer") @@ -10436,6 +10510,38 @@ expression information. The package functions as a wrapper for Startrac and powerTCR R packages.") (license license:gpl2))) +(define-public r-scrnaseq + (package + (name "r-scrnaseq") + (version "2.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scRNAseq" version + 'experiment)) + (sha256 + (base32 "0dbh3sqq7lkkdf7vls5qg7fbn6y74c7hsigb4d69pvk934ll88aw")))) + (properties `((upstream-name . "scRNAseq"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-annotationhub + r-biocgenerics + r-ensembldb + r-experimenthub + r-genomicfeatures + r-genomicranges + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scRNAseq") + (synopsis "Collection of public single-cell RNA-seq datasets") + (description + "This package contains gene-level counts for a collection of public +@code{scRNA-seq} datasets, provided as @code{SingleCellExperiment} objects +with cell- and gene-level metadata.") + (license license:cc0))) + (define-public r-scry (package (name "r-scry") @@ -10793,6 +10899,44 @@ identifier translation via the GDC API.") "This package implements widgets to provide user interfaces.") (license license:artistic2.0))) +(define-public r-toast + (package + (name "r-toast") + (version "1.16.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "TOAST" version)) + (sha256 + (base32 "00wpgs2zdrgrh9xmp6m5h9xgv85mhdi36qvwg9gwbz9i7cfabmy1")))) + (properties `((upstream-name . "TOAST"))) + (build-system r-build-system) + (propagated-inputs (list r-corpcor + r-doparallel + r-epidish + r-ggally + r-ggplot2 + r-limma + r-nnls + r-quadprog + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TOAST") + (synopsis "Tools for the analysis of heterogeneous tissues") + (description + "This package is devoted to analyzing high-throughput data (e.g. gene +expression microarray, DNA methylation microarray, RNA-seq) from complex +tissues. Current functionalities include + +@enumerate +@item detect cell-type specific or cross-cell type differential signals +@item tree-based differential analysis +@item improve variable selection in reference-free deconvolution +@item partial reference-free deconvolution with prior knowledge. +@end enumerate") + (license license:gpl2))) + ;; TODO: check javascript (define-public r-trackviewer (package |