sparrow
This is the released version of sparrow; for the devel version, see sparrow.
Take command of set enrichment analyses through a unified interface
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| 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, KernSmooth, knitr, magrittr, matrixStats, msigdbr (>= 10.0), orthogene, 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_1.18.0.tar.gz |
| Windows Binary (x86_64) | sparrow_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | sparrow_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | sparrow_1.18.0.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 |