roastgsa

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see roastgsa.

Rotation based gene set analysis

Bioconductor version: 3.21

This package implements a variety of functions useful for gene set analysis using rotations to approximate the null distribution. It contributes with the implementation of seven test statistic scores that can be used with different goals and interpretations. Several functions are available to complement the statistical results with graphical representations.

Author: Adria Caballe [aut, cre] ORCID iD ORCID: 0000-0002-2388-4713

Maintainer: Adria Caballe <adria.caballe at irbbarcelona.org>

Citation (from within R, enter citation("roastgsa")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("roastgsa")

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("roastgsa")

roastgsa vignette (gene set collections) HTML R Script

roastgsa vignette (main) HTML R Script

roastgsa vignette (RNAseq) HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

Version 1.6.0

In Bioconductor since BioC 3.18 (R-4.3) (2 years)

License GPL-3

Depends R (>= 4.3.0)

Imports parallel, grDevices, graphics, utils, stats, methods, grid, RColorBrewer, gplots, ggplot2, limma, Biobase

System Requirements

URL

Bug Reports https://github.com/adricaba/roastgsa/issues

Suggests BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2

Linking To

Enhances

Depends On Me

Imports Me

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package roastgsa_1.6.0.tar.gz

Windows Binary (x86_64) roastgsa_1.6.0.zip (64-bit only)

macOS Binary (x86_64) roastgsa_1.6.0.tgz

macOS Binary (arm64) roastgsa_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/roastgsa

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/roastgsa

Bioc Package Browser https://code.bioconductor.org/browse/roastgsa/

Package Short Url https://bioconductor.org/packages/roastgsa/

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