ClustIRR analyzes repertoires of B- and T-cell receptors. It begins the analysis by identifying communities (i.e., specificity groups) 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 factors such as infection or cancer treatment.
ClustIRR is an R-package available from Bioconductor:
https://bioconductor.org/packages/ClustIRR/
To install this package, start R and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ClustIRR")To use the development version of ClustIRR you can install it from Github. To do this, start R and enter:
library(devtools)
install_github("snaketron/ClustIRR")Case studies are provided in the directory /vignettes
