sparrow
Take command of set enrichment analyses through a unified interface
Bioconductor version: 3.23 · Package version: 1.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sparrow")Details
| Maintainer | Steve Lianoglou <slianoglou@gmail.com> |
| Author | Steve Lianoglou [aut, cre] (ORCID: <https://orcid.org/0000-0002-0924-1754>), Arkadiusz Gladki [ctb], Aratus Informatics, LLC [fnd] (2023+), Denali Therapeutics [fnd] (2018-2022), Genentech [fnd] (2014 - 2017) |
| License | MIT + file LICENSE |
| URL | https://github.com/lianos/sparrow |
| Bug Reports | https://github.com/lianos/sparrow/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | GeneSetEnrichment, Pathways, Software |
| Package Short Url | https://bioconductor.org/packages/sparrow/ |
Citation
From within R, enter citation("sparrow"):
Steve Lianoglou. sparrow: Take command of set enrichment analyses through a unified interface. doi:10.18129/B9.bioc.sparrow, R package version 1.18.0, https://bioconductor.org/packages/sparrow.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | sparrow_1.18.0.tgz |
| macOS binary (x86_64) | sparrow_1.18.0.tgz |
Dependencies
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
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
Reverse dependencies
Suggests Me (1): gCrisprTools