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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SeqGSEA")
In most cases, you don't need to download the package archive at all.
SeqGSEA
|
This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SeqGSEA.
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Bioconductor version: 3.0
The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.
Author: Xi Wang <Xi.Wang at newcastle.edu.au>
Maintainer: Xi Wang <Xi.Wang at mdc-berlin.de>
Citation (from within R,
enter citation("SeqGSEA")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SeqGSEA")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SeqGSEA")
| R Script | Gene set enrichment analysis of RNA-Seq data with the SeqGSEA package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, GeneExpression, GeneSetEnrichment, RNASeq, Sequencing, Software |
| Version | 1.6.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | GPL (>= 3) |
| Depends | Biobase, doParallel, DESeq |
| Imports | methods, biomaRt |
| LinkingTo | |
| Suggests | easyRNASeq, GenomicRanges |
| 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 | SeqGSEA_1.6.0.tar.gz |
| Windows Binary | SeqGSEA_1.6.0.zip |
| Mac OS X 10.6 (Snow Leopard) | SeqGSEA_1.6.0.tgz |
| Mac OS X 10.9 (Mavericks) | SeqGSEA_1.6.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/SeqGSEA/tree/release-3.0 |
| Package Short Url | http://bioconductor.org/packages/SeqGSEA/ |
| Package Downloads Report | Download Stats |
Documentation »
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