DEXSeq
This is the development version of DEXSeq; for the stable release version, see DEXSeq.
Inference of differential exon usage in RNA-Seq
Bioconductor version: Development (3.21)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DEXSeq")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Visualization |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (13 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 |
| System Requirements | |
| URL |
See More
| Suggests | GenomicFeatures, txdbmaker, pasilla(>= 0.2.22), parathyroidSE, BiocStyle, knitr, rmarkdown, testthat, pasillaBamSubset, GenomicAlignments, roxygen2, glmGamPoi |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/DEXSeq |
| Source Repository (Developer Access) | git clone [email protected]:packages/DEXSeq |
| Package Short Url | https://bioconductor.org/packages/DEXSeq/ |
| Package Downloads Report | Download Stats |