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

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
See More
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 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