IgGeneUsage
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see IgGeneUsage.
Differential gene usage in immune repertoires
Bioconductor version: 3.18
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("IgGeneUsage")):
Installation
To install this package, start R (version "4.3") 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, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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, tidyr |
| System Requirements | GNU make |
| URL | https://github.com/snaketron/IgGeneUsage |
| Bug Reports | https://github.com/snaketron/IgGeneUsage/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2, ggforce, gridExtra, ggrepel |
| 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) |
| 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_1.16.0.tar.gz |
| Windows Binary | IgGeneUsage_1.16.0.zip (64-bit only) |
| macOS Binary (x86_64) | IgGeneUsage_1.16.0.tgz |
| macOS Binary (arm64) | IgGeneUsage_1.16.0.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 |