To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("rgsepd")
In most cases, you don't need to download the package archive at all.
rgsepd
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Gene Set Enrichment / Projection Displays
Bioconductor version: Release (3.1)
R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq 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 and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("rgsepd")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rgsepd")
| R Script | An Introduction to the rgsepd package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneSetEnrichment, RNASeq, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 3.0.0), DESeq2, goseq(>= 1.17) |
| Imports | gplots, biomaRt, org.Hs.eg.db, GO.db, GenomicRanges, hash, AnnotationDbi |
| LinkingTo | |
| Suggests | boot, tools, RUnit, BiocGenerics, knitr, xtable |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rgsepd_1.0.0.tar.gz |
| Windows Binary | rgsepd_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | rgsepd_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | rgsepd_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/rgsepd/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/rgsepd/ |
| Package Downloads Report | Download Stats |
Documentation »
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