sparrow

Take command of set enrichment analyses through a unified interface

Bioconductor version: Release (3.19)

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], 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 "4.4") 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	1.10.1
In Bioconductor since	BioC 3.14 (R-4.1) (3 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
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, magrittr, matrixStats, msigdbr (>= 7.4.1), KernSmooth, knitr, PANTHER.db(>= 1.0.3), R.utils, reactome.db, rmarkdown, SummarizedExperiment, statmod, stringr, testthat, webshot
Linking To
Enhances
Depends On Me
Imports Me	signifinder
Suggests Me	gCrisprTools
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	sparrow_1.10.1.tar.gz
Windows Binary (x86_64)	sparrow_1.10.1.zip
macOS Binary (x86_64)	sparrow_1.10.1.tgz
macOS Binary (arm64)	sparrow_1.10.1.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