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Bioconductor - sparrow (development version)

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 (3.22)

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: 0000-0002-0924-1754 , 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 "4.5") 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")

Details biocViews GeneSetEnrichment, Pathways, Software Version 1.15.0 In Bioconductor since BioC 3.14 (R-4.1) (3.5 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.

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