doseR
doseR
Bioconductor version: Release (3.20)
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("doseR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, DifferentialExpression, GeneExpression, Infrastructure, Sequencing, Software, SystemsBiology |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 years) |
| License | GPL |
| Depends | R (>= 3.6) |
| Imports | edgeR, methods, stats, graphics, matrixStats, mclust, lme4, RUnit, SummarizedExperiment, digest, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| 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 | doseR_1.22.0.tar.gz |
| Windows Binary (x86_64) | doseR_1.22.0.zip |
| macOS Binary (x86_64) | doseR_1.22.0.tgz |
| macOS Binary (arm64) | doseR_1.22.0.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 |