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rgsepd

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

Gene Set Enrichment / Projection Displays


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

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

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 1.37.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-3
Depends R (>= 4.2.0), DESeq2, goseq(>= 1.28)
Imports gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi
System Requirements
URL
See More
Suggests boot, tools, BiocGenerics, knitr, xtable
Linking To
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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 rgsepd_1.37.0.tar.gz
Windows Binary rgsepd_1.37.0.zip (64-bit only)
macOS Binary (x86_64) rgsepd_1.37.0.tgz
macOS Binary (arm64) rgsepd_1.37.0.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