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roastgsa

This is the development version of roastgsa; for the stable release version, see roastgsa.

Rotation based gene set analysis


Bioconductor version: Development (3.19)

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]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, Cheminformatics, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, Epigenetics, ExonArray, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, Metabolomics, MicroRNAArray, Microarray, MultipleComparison, Normalization, OneChannel, Pathways, Preprocessing, ProprietaryPlatforms, Proteomics, QualityControl, RNASeq, Regression, Sequencing, Software, Survival, SystemsBiology, TimeCourse, Transcription, Transcriptomics, TwoChannel, mRNAMicroarray
Version 1.1.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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
See More
Suggests BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package roastgsa_1.1.0.tar.gz
Windows Binary roastgsa_1.1.0.zip (64-bit only)
macOS Binary (x86_64) roastgsa_1.1.0.tgz
macOS Binary (arm64)
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/
Package Downloads Report Download Stats