IgGeneUsage

DOI: 10.18129/B9.bioc.IgGeneUsage    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: 3.10

Decoding the properties of immune repertoires is key in understanding the response of adaptive immunity to challenges such as viral infection. One important task in immune repertoire profiling is the detection of biases in Ig gene usage between biological conditions. IgGeneUsage is a computational tool for the analysis of differential gene usage in immune repertoires. It employs Bayesian hierarchical models to fit complex gene usage data from immune repertoire sequencing experiments and quantifies Ig gene usage biases as probabilities.

Author: Simo Kitanovski [aut, cre]

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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	1.0.1
In Bioconductor since	BioC 3.10 (R-3.6) (< 6 months)
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_1.0.1.tar.gz
Windows Binary	IgGeneUsage_1.0.1.zip
Mac OS X 10.11 (El Capitan)	IgGeneUsage_1.0.1.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