sparrow

This is the released version of sparrow; for the devel version, see sparrow.

Take command of set enrichment analyses through a unified interface

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DOI: 10.18129/B9.bioc.sparrow

Bioconductor version: Release (3.22)

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.

Author: Steve Lianoglou [aut, cre] ORCID iD ORCID: 0000-0002-0924-1754 , Arkadiusz Gladki [ctb], Aratus Informatics, LLC [fnd] (2023+), Denali Therapeutics [fnd] (2018-2022), Genentech [fnd] (2014 - 2017)

Maintainer: Steve Lianoglou <slianoglou at gmail.com>

Citation (from within R, enter citation("sparrow")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("sparrow")

Performing gene set enrichment analyses with sparrow HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneSetEnrichment, Pathways, Software

Version 1.16.0

In Bioconductor since BioC 3.14 (R-4.1) (4 years)

License MIT + file LICENSE

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

System Requirements

URL https://github.com/lianos/sparrow

Bug Reports https://github.com/lianos/sparrow/issues

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

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sparrow_1.16.0.tar.gz

Windows Binary (x86_64) sparrow_1.16.0.zip

macOS Binary (x86_64) sparrow_1.16.0.tgz

macOS Binary (arm64) sparrow_1.16.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/sparrow

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sparrow

Bioc Package Browser https://code.bioconductor.org/browse/sparrow/

Package Short Url https://bioconductor.org/packages/sparrow/

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