DOI: 10.18129/B9.bioc.IgGeneUsage    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: 3.12

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>

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biocViews Bayesian, DifferentialExpression, Genetics, Regression, Software
Version 1.4.0
In Bioconductor since BioC 3.10 (R-3.6) (1.5 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)
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel
BugReports https://github.com/snaketron/IgGeneUsage/issues
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Source Package IgGeneUsage_1.4.0.tar.gz
Windows Binary IgGeneUsage_1.3.1.zip
macOS 10.13 (High Sierra) IgGeneUsage_1.4.1.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/
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