ClustIRR
This is the development version of ClustIRR; for the stable release version, see ClustIRR.
Clustering of immune receptor repertoires
Bioconductor version: Development (3.21)
ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.
Author: Simo Kitanovski [aut, cre] (ORCID:
Maintainer: Simo Kitanovski <simokitanovski at gmail.com>
citation("ClustIRR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ClustIRR")
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("ClustIRR")| Analysis of T and B cell receptor repertoires with ClustIRR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Classification, Clustering, ImmunoOncology, SingleCell, Software |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | blaster, future, future.apply, grDevices, igraph, methods, pwalign, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, visNetwork |
| System Requirements | GNU make |
| URL | https://github.com/snaketron/ClustIRR |
| Bug Reports | https://github.com/snaketron/ClustIRR/issues |
See More
| Suggests | BiocStyle, knitr, testthat, ggplot2, ggrepel, patchwork |
| 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 | ClustIRR_1.5.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ClustIRR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ClustIRR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ClustIRR/ |
| Package Short Url | https://bioconductor.org/packages/ClustIRR/ |
| Package Downloads Report | Download Stats |