To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DEXSeq")
In most cases, you don't need to download the package archive at all.
DEXSeq
Inference of differential exon usage in RNA-Seq
Bioconductor version: 3.0
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>
Citation (from within R,
enter citation("DEXSeq")):
Installation
To install this package, start R and enter:
source("http://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 | DifferentialExpression, RNASeq, Sequencing, Software |
| Version | 1.12.2 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | GPL (>= 3) |
| Depends | Biobase, GenomicRanges, IRanges, DESeq2(>= 1.5.63), BiocParallel |
| Imports | BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter, RColorBrewer |
| LinkingTo | |
| Suggests | GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | parathyroid |
| Imports Me | |
| Suggests Me | GenomicRanges, oneChannelGUI, pasilla |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DEXSeq_1.12.2.tar.gz |
| Windows Binary | DEXSeq_1.12.2.zip |
| Mac OS X 10.6 (Snow Leopard) | DEXSeq_1.12.2.tgz |
| Mac OS X 10.9 (Mavericks) | DEXSeq_1.12.2.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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