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Bioconductor - ClustIRR (development version)

ClustIRR

This is the development version of ClustIRR; for the stable release version, see ClustIRR.

Clustering of immune receptor repertoires

Bioconductor version: Development (3.22)

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: 0000-0003-2909-5376 , Kai Wollek [aut] ORCID: 0009-0008-5941-9160

Maintainer: Simo Kitanovski <simokitanovski at gmail.com>

Citation (from within R, enter 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")

Decoding T- and B-cell receptor repertoires with ClustIRR HTML R Script Reference Manual PDF NEWS Text LICENSE Text Details biocViews Bayesian, BiomedicalInformatics, Classification, Clustering, ImmunoOncology, MathematicalBiology, SingleCell, Software Version 1.7.1 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) License GPL-3 + file LICENSE Depends R (>= 4.3.0) Imports blaster, future, future.apply, grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales 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.

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