roastgsa
Rotation based gene set analysis
Bioconductor version: Release (3.18)
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("roastgsa")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
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 | 1.0.0 |
| 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_1.0.0.tar.gz |
| Windows Binary | roastgsa_1.0.0.zip |
| macOS Binary (x86_64) | roastgsa_1.0.0.tgz |
| macOS Binary (arm64) | roastgsa_1.0.0.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/ |
| Package Downloads Report | Download Stats |