IgGeneUsage

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: 3.21

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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software

Version 1.22.0

In Bioconductor since BioC 3.10 (R-3.6) (6 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

Suggests BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, ggrepel, patchwork

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_1.22.0.tar.gz

Windows Binary (x86_64) IgGeneUsage_1.22.0.zip

macOS Binary (x86_64) IgGeneUsage_1.22.0.tgz

macOS Binary (arm64) IgGeneUsage_1.22.0.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/

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