DOI: 10.18129/B9.bioc.IgGeneUsage  

This is the development version of IgGeneUsage; for the stable release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: Development (3.18)

Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.

Author: Simo Kitanovski [aut, cre]

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

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


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

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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


biocViews Bayesian, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.2.0)
Imports methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0), SummarizedExperiment
LinkingTo BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>=, RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel
SystemRequirements GNU make
URL https://github.com/snaketron/IgGeneUsage
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_1.15.0.tar.gz
Windows Binary IgGeneUsage_1.15.0.zip
macOS Binary (x86_64) IgGeneUsage_1.15.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/IgGeneUsage
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IgGeneUsage
Bioc Package Browser https://code.bioconductor.org/browse/IgGeneUsage/
Package Short Url https://bioconductor.org/packages/IgGeneUsage/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: