IgGeneUsage
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.
Differential gene usage in immune repertoires
Bioconductor version: 3.14
Detection of biases in immunoglobulin (Ig) gene usage between adaptive immune repertoires that belong to different biological conditions is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage using probabilistic model which is analyzed computationally by Bayes inference.
Author: Simo Kitanovski [aut, cre]
Maintainer: Simo Kitanovski <simo.kitanovski at uni-due.de>
citation("IgGeneUsage")):
Installation
To install this package, start R (version "4.1") 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 | 1.8.0 |
| 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_1.8.0.tar.gz |
| Windows Binary | |
| macOS 10.13 (High Sierra) | IgGeneUsage_1.8.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |