doseR

DOI: 10.18129/B9.bioc.doseR    

doseR

Bioconductor version: Release (3.13)

doseR package is a next generation sequencing package for sex chromosome dosage compensation which can be applied broadly to detect shifts in gene expression among an arbitrary number of pre-defined groups of loci. doseR is a differential gene expression package for count data, that detects directional shifts in expression for multiple, specific subsets of genes, broad utility in systems biology research. doseR has been prepared to manage the nature of the data and the desired set of inferences. doseR uses S4 classes to store count data from sequencing experiment. It contains functions to normalize and filter count data, as well as to plot and calculate statistics of count data. It contains a framework for linear modeling of count data. The package has been tested using real and simulated data.

Author: AJ Vaestermark, JR Walters.

Maintainer: ake.vastermark <ake.vastermark at gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("doseR")

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("doseR")

 

HTML	R Script	doseR
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, Sequencing, Software, SystemsBiology
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL
Depends	R (>= 3.6)
Imports	edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	doseR_1.8.0.tar.gz
Windows Binary	doseR_1.8.0.zip
macOS 10.13 (High Sierra)	doseR_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/doseR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/doseR
Package Short Url	https://bioconductor.org/packages/doseR/
Package Downloads Report	Download Stats