IgGeneUsage

DOI: 10.18129/B9.bioc.IgGeneUsage    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: 3.14

Detection of biases in immunoglobulin (Ig) gene usage between adaptive immune repertoires that belong to different biological conditions is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage using probabilistic model which is analyzed computationally by Bayes inference.

Author: Simo Kitanovski [aut, cre]

Maintainer: Simo Kitanovski <simo.kitanovski at uni-due.de>

Installation

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

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

BiocManager::install("IgGeneUsage")

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("IgGeneUsage")

 

HTML	R Script	User Manual: IgGeneUsage
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Bayesian, DifferentialExpression, Genetics, Regression, Software
Version	1.8.0
In Bioconductor since	BioC 3.10 (R-3.6) (2.5 years)
License	file LICENSE
Depends	methods, R (>= 3.6.0), Rcpp (>= 0.12.0), SummarizedExperiment, StanHeaders (> 2.18.1)
Imports	rstan (>= 2.19.2), reshape2 (>= 1.4.3)
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel
SystemRequirements
Enhances
URL
BugReports	https://github.com/snaketron/IgGeneUsage/issues
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	IgGeneUsage_1.8.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	IgGeneUsage_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/IgGeneUsage
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/IgGeneUsage
Package Short Url	https://bioconductor.org/packages/IgGeneUsage/
Package Downloads Report	Download Stats