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ClustIRR

Clustering of immune receptor repertoires


Bioconductor version: Release (3.19)

ClustIRR is a quantitative method for clustering of immune receptor repertoires (IRRs). The algorithm identifies groups of T or B cell receptors (TCRs or BCRs) with possibly similar specificity directly from the sequences of their complementarity determining regions. ClustIRR uses graphs to visualize the specificity structures of IRRs.

Author: Simo Kitanovski [aut, cre] , Kai Wollek [aut]

Maintainer: Simo Kitanovski <simokitanovski at gmail.com>

Citation (from within R, enter citation("ClustIRR")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")
Introduction to ClustIRR HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Classification, Clustering, ImmunoOncology, SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.3.0)
Imports stringdist, methods, stats, utils, igraph, visNetwork, blaster, pwalign, grDevices, parallel
System Requirements
URL https://github.com/snaketron/ClustIRR
Bug Reports https://github.com/snaketron/ClustIRR/issues
See More
Suggests BiocStyle, knitr, testthat, ggplot2, patchwork, ggrepel
Linking To
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ClustIRR_1.2.0.tar.gz
Windows Binary ClustIRR_1.2.0.zip (64-bit only)
macOS Binary (x86_64) ClustIRR_1.2.0.tgz
macOS Binary (arm64) ClustIRR_1.2.0.tgz
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