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doseR

doseR


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("doseR")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
doseR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, Sequencing, Software, SystemsBiology
Version 1.18.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL
Depends R (>= 3.6)
Imports edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors
System Requirements
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Suggests BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package doseR_1.18.0.tar.gz
Windows Binary doseR_1.18.0.zip (64-bit only)
macOS Binary (x86_64) doseR_1.18.0.tgz
macOS Binary (arm64) doseR_1.18.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/doseR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/doseR
Bioc Package Browser https://code.bioconductor.org/browse/doseR/
Package Short Url https://bioconductor.org/packages/doseR/
Package Downloads Report Download Stats