IgGeneUsage

DOI: 10.18129/B9.bioc.IgGeneUsage    

This is the development version of IgGeneUsage; for the stable release version, see IgGeneUsage.

Differential gene usage in immune repertoires

Bioconductor version: Development (3.11)

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>

Citation (from within R, enter citation("IgGeneUsage")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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Details

biocViews Bayesian, DifferentialExpression, Genetics, Regression, Software
Version 1.1.1
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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)
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel
SystemRequirements
Enhances
URL
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_1.1.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) IgGeneUsage_1.1.1.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/
Package Downloads Report Download Stats

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