rgsepd
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see rgsepd.
Gene Set Enrichment / Projection Displays
Bioconductor version: 3.10
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("rgsepd")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Software |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), DESeq2, goseq(>= 1.28) |
| Imports | gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, hash, AnnotationDbi |
| System Requirements | |
| URL |
See More
| Suggests | boot, tools, BiocGenerics, knitr, xtable |
| 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 | rgsepd_1.18.0.tar.gz |
| Windows Binary | rgsepd_1.18.0.zip |
| Mac OS X 10.11 (El Capitan) | rgsepd_1.18.0.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 |
| Old Source Packages for BioC 3.10 | Source Archive |