IgGeneUsage

DOI: 10.18129/B9.bioc.IgGeneUsage  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Bayesian, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software
Version	1.12.0
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 (>= 0.3.3.3.0), 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
Enhances
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_1.12.0.tar.gz
Windows Binary	IgGeneUsage_1.12.0.zip
macOS Binary (x86_64)	IgGeneUsage_1.12.0.tgz
macOS Binary (arm64)	IgGeneUsage_1.12.0.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