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IgGeneUsage

Differential gene usage in immune repertoires


Bioconductor version: Release (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")):

Installation

To install this package, start R (version "4.3") 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")
User Manual: IgGeneUsage HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Bayesian, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software
Version 1.16.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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, tidyr
System Requirements GNU make
URL https://github.com/snaketron/IgGeneUsage
Bug Reports https://github.com/snaketron/IgGeneUsage/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel
Linking To BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package IgGeneUsage_1.16.0.tar.gz
Windows Binary IgGeneUsage_1.16.0.zip
macOS Binary (x86_64) IgGeneUsage_1.16.0.tgz
macOS Binary (arm64) IgGeneUsage_1.16.0.tgz
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