IgGeneUsage
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.
Differential gene usage in immune repertoires
Bioconductor version: 3.10
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("IgGeneUsage")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, DifferentialExpression, Genetics, Regression, Software |
| Version | 1.0.1 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| 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) |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/snaketron/IgGeneUsage/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IgGeneUsage_1.0.1.tar.gz |
| Windows Binary | IgGeneUsage_1.0.1.zip |
| Mac OS X 10.11 (El Capitan) | IgGeneUsage_1.0.1.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 |
| Old Source Packages for BioC 3.10 | Source Archive |