DOI: 10.18129/B9.bioc.IgGeneUsage  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: 3.17

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>

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biocViews Bayesian, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software
Version 1.14.0
In Bioconductor since BioC 3.10 (R-3.6) (4 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
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Source Package IgGeneUsage_1.14.0.tar.gz
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