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("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 | ||
| 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 (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 |