IgGeneUsage
Differential gene usage in immune repertoires
Bioconductor version: 3.24 · Package version: 1.27.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IgGeneUsage")Details
| Maintainer | Simo Kitanovski <simo.kitanovski@uni-due.de> |
| Author | Simo Kitanovski [aut, cre] |
| License | MIT + file LICENSE |
| URL | https://github.com/snaketron/IgGeneUsage |
| Bug Reports | https://github.com/snaketron/IgGeneUsage/issues |
| System Requirements | GNU make |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, BiomedicalInformatics, DifferentialExpression, Genetics, ImmunoOncology, MathematicalBiology, Regression, Software |
| Package Short Url | https://bioconductor.org/packages/IgGeneUsage/ |
Citation
From within R, enter citation("IgGeneUsage"):
Simo Kitanovski. IgGeneUsage: Differential gene usage in immune repertoires. doi:10.18129/B9.bioc.IgGeneUsage, R package version 1.27.0, https://bioconductor.org/packages/IgGeneUsage.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | IgGeneUsage_1.27.0.tar.gz |
| Windows binary (x86_64) | IgGeneUsage_1.27.0.zip |
| macOS binary (arm64) | IgGeneUsage_1.27.0.tgz |
| macOS binary (x86_64) | IgGeneUsage_1.27.0.tgz |
Dependencies
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
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, ggrepel, patchwork