To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
In most cases, you don't need to download the package archive at all.
DEXSeq
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see DEXSeq.
Inference of differential exon usage in RNA-Seq
Bioconductor version: 3.4
The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.
Author: Simon Anders <sanders at fs.tum.de> and Alejandro Reyes <alejandro.reyes at embl.de>
Maintainer: Alejandro Reyes <alejandro.reyes at embl.de>
Citation (from within R,
enter citation("DEXSeq")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DEXSeq")
| R Script | Analyzing RNA-seq data for differential exon usage with the "DEXSeq" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Sequencing, Software, Visualization |
| Version | 1.20.2 |
| In Bioconductor since | BioC 2.9 (R-2.14) (5.5 years) |
| License | GPL (>= 3) |
| Depends | BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.9.11), AnnotationDbi, RColorBrewer, S4Vectors |
| Imports | BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter |
| LinkingTo | |
| Suggests | GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | ASpli |
| Imports Me | |
| Suggests Me | GenomicRanges, JctSeqData, oneChannelGUI, pasilla, subSeq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DEXSeq_1.20.2.tar.gz |
| Windows Binary | DEXSeq_1.20.2.zip |
| Mac OS X 10.9 (Mavericks) | DEXSeq_1.20.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/DEXSeq/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/DEXSeq/ |
| Package Downloads Report | Download Stats |
Documentation »
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