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snaketron / ClustIRR

Clustering of immune receptor repertoires
GNU General Public License v3.0
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b-cell-receptor bioinformatics clustering immunoinformatics immunology quantitative-methods rep-seq repertoire-analysis t-cell-receptor

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ClustIRR: Clustering of Immune Receptor Repertoires

Overview

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) that likely have the same antigen specificity. This is achieved by comparing global and local sequence features of the complementarity determining regions (CDRs) of TCRs and BCRs. Once the specificity groups are identified in a set of IRRs, the algorithm identifies clusters and performs a quantitative comparison of the cluster abundances between biological conditions.

How to use ClustIRR

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

Workflow & output

clustirr workflow