roastgsa

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	roastgsa vignette (gene set collections)
HTML	R Script	roastgsa vignette (main)
HTML	R Script	roastgsa vignette (RNAseq)
PDF		Reference Manual
Text		NEWS

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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, GSEABenchmarkeR, EnrichmentBrowser, preprocessCore, DESeq2
SystemRequirements
Enhances
URL
BugReports	https://github.com/adricaba/roastgsa/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
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
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