sparrow
This is the development version of sparrow; for the stable release version, see sparrow.
Take command of set enrichment analyses through a unified interface
Bioconductor version: Development (3.21)
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:
Maintainer: Steve Lianoglou <slianoglou at gmail.com>
citation("sparrow")
):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.13.4 |
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 | |
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_1.13.4.tar.gz |
Windows Binary (x86_64) | sparrow_1.13.4.zip |
macOS Binary (x86_64) | sparrow_1.13.4.tgz |
macOS Binary (arm64) | sparrow_1.13.4.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 |