DEXSeq
Inference of differential exon usage in RNA-Seq
Bioconductor version: Release (2.11)
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>, both at EMBL Heidelberg
Maintainer: Alejandro Reyes <alejandro.reyes at embl.de>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
To cite this package in a publication, start R and enter:
citation("DEXSeq")
Documentation
| R Script | Analyzing RNA-seq data for differential exon usage with the "DEXSeq" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, HighThroughputSequencing, RNAseq, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>= 3) |
| Depends | Biobase(>= 2.13.11) |
| Imports | biomaRt, hwriter, methods, stringr, statmod (>= 1.4.15) |
| Suggests | pasilla(>= 0.2.13) |
| System Requirements | |
| URL | |
| Depends On Me | pasilla |
| Imports Me | |
| Suggests Me | GenomicRanges |
Package Downloads
| Package Source | DEXSeq_1.4.0.tar.gz |
| Windows Binary | DEXSeq_1.4.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) | DEXSeq_1.4.0.tgz |
| Package Downloads Report | Download Stats |
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