sparrow

Take command of set enrichment analyses through a unified interface

Bioconductor version: Release (3.17)

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] , Arkadiusz Gladki [ctb], Denali Therapeutics [fnd] (2018+), 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 "4.3") 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

Details

biocViews	GeneSetEnrichment, Pathways, Software
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.0)
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
Linking To
Suggests	AnnotationDbi, BiasedUrn, Biobase(>= 2.24.0), BiocStyle, DESeq2, dplyr, dtplyr, fgsea, GSVA, GO.db, goseq, hexbin, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db(>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot
System Requirements
Enhances
URL	https://github.com/lianos/sparrow
Bug Reports	https://github.com/lianos/sparrow/issues

Depends On Me
Imports Me
Suggests Me	gCrisprTools
Links To Me
Build Report

Package Archives

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

Source Package	sparrow_1.6.0.tar.gz
Windows Binary	sparrow_1.6.0.zip
macOS Binary (x86_64)	sparrow_1.6.0.tgz
macOS Binary (arm64)	sparrow_1.6.0.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/
Package Downloads Report	Download Stats