DEXSeq
Inference of differential exon usage in RNA-Seq
Bioconductor version: Release (3.17)
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.ds at gmail.com>
Maintainer: Alejandro Reyes <alejandro.reyes.ds at gmail.com>
citation("DEXSeq")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DEXSeq")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DEXSeq")| Inferring differential exon usage in RNA-Seq data with the DEXSeq package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (12 years) |
| License | GPL (>= 3) |
| Depends | BiocParallel, Biobase, SummarizedExperiment, IRanges(>= 2.5.17), GenomicRanges(>= 1.23.7), DESeq2(>= 1.39.6), AnnotationDbi, RColorBrewer, S4Vectors(>= 0.23.18) |
| Imports | BiocGenerics, biomaRt, hwriter, methods, stringr, Rsamtools, statmod, geneplotter, genefilter |
| Linking To | |
| Suggests | GenomicFeatures(>= 1.13.29), pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2 |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | IsoformSwitchAnalyzeR, pasilla, rnaseqDTU |
| Imports Me | diffUTR, IntEREst, pairedGSEA |
| Suggests Me | bambu, BioPlex, GenomicRanges, satuRn, stageR, subSeq |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DEXSeq_1.46.0.tar.gz |
| Windows Binary | DEXSeq_1.46.0.zip |
| macOS Binary (x86_64) | DEXSeq_1.46.0.tgz |
| macOS Binary (arm64) | DEXSeq_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DEXSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DEXSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/DEXSeq/ |
| Package Short Url | https://bioconductor.org/packages/DEXSeq/ |
| Package Downloads Report | Download Stats |