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rgsepd

Gene Set Enrichment / Projection Displays

Bioconductor version: Release (3.17)

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

Author: Karl Stamm

Maintainer: Karl Stamm <karl.stamm at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

BiocManager::install("rgsepd")

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("rgsepd")
An Introduction to the rgsepd package PDF R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Software
Version 1.32.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL-3
Depends R (>= 4.2.0), DESeq2, goseq(>= 1.28)
Imports gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi
Linking To
Suggests boot, tools, BiocGenerics, knitr, xtable
System Requirements
Enhances
URL
See More
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 rgsepd_1.32.0.tar.gz
Windows Binary rgsepd_1.32.0.zip
macOS Binary (x86_64) rgsepd_1.32.0.tgz
macOS Binary (arm64) rgsepd_1.32.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/rgsepd
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/rgsepd
Bioc Package Browser https://code.bioconductor.org/browse/rgsepd/
Package Short Url https://bioconductor.org/packages/rgsepd/
Package Downloads Report Download Stats