sparrow

Take command of set enrichment analyses through a unified interface

Bioconductor version: 3.23 · Package version: 1.18.0

Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sparrow")

Details

Maintainer	Steve Lianoglou <slianoglou@gmail.com>
Author	Steve Lianoglou [aut, cre] (ORCID: <https://orcid.org/0000-0002-0924-1754>), Arkadiusz Gladki [ctb], Aratus Informatics, LLC [fnd] (2023+), Denali Therapeutics [fnd] (2018-2022), Genentech [fnd] (2014 - 2017)
License	MIT + file LICENSE
URL	https://github.com/lianos/sparrow
Bug Reports	https://github.com/lianos/sparrow/issues
Downloads rank	521
Source branch	RELEASE_3_23
biocViews	GeneSetEnrichment, Pathways, Software

Documentation

Performing gene set enrichment analyses with sparrow

Download

Source package

Dependencies

Depends: R (>= 4.1.0)

Imports: babelgene (>= 21.4), BiocGenerics, BiocParallel, BiocSet, checkmate, circlize, ComplexHeatmap (>= 2.0), data.table (>= 1.10.4), DelayedMatrixStats, edgeR (>= 3.18.1), ggplot2 (>= 2.2.0), graphics, grDevices, GSEABase, irlba, limma, Matrix, methods, plotly (>= 4.9.0), stats, utils, viridis

Suggests: AnnotationDbi, BiasedUrn, Biobase (>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0), orthogene, PANTHER.db (>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot

Reverse dependencies

Suggests Me (1): gCrisprTools