Package: ClustIRR 1.5.39

Simo Kitanovski

ClustIRR: Clustering of immune receptor repertoires

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.

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

ClustIRR_1.5.39.tar.gz
ClustIRR_1.5.39.zip(r-4.5)ClustIRR_1.5.39.zip(r-4.4)ClustIRR_1.5.39.zip(r-4.3)
ClustIRR_1.5.39.tgz(r-4.4-x86_64)ClustIRR_1.5.39.tgz(r-4.4-arm64)ClustIRR_1.5.39.tgz(r-4.3-x86_64)ClustIRR_1.5.39.tgz(r-4.3-arm64)
ClustIRR_1.5.39.tar.gz(r-4.5-noble)ClustIRR_1.5.39.tar.gz(r-4.4-noble)
ClustIRR.pdf |ClustIRR.html✨
ClustIRR/json (API)
NEWS

# Install 'ClustIRR' in R:

install.packages('ClustIRR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/snaketron/clustirr/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

BLOSUM62 - BLOSUM62 matrix
CDR3ab - Mock data set of complementarity determining region 3 (CDR3) sequences and variable (V) and joining (J) genes from the alpha and beta chains of 10,000 T cell receptors.
mcpas - CDR3 sequences and their matching epitopes obtained from McPAS-TCR
tcr3d - CDR3 sequences and their matching epitopes obtained from TCR3d
vdjdb - CDR3 sequences and their matching epitopes obtained from VDJdb

On BioConductor:ClustIRR-1.5.24(bioc 3.21)ClustIRR-1.4.0(bioc 3.20)

clustering immunooncology singlecell software classification b-cell-receptor bioinformatics immunoinformatics immunology quantitative-methods rep-seq repertoire-analysis t-cell-receptor cpp

5.95 score 2 stars 2 scripts 173 downloads 11 exports 98 dependencies

Last updated 10 days agofrom:bf0fdba123. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 24 2025
R-4.5-win-x86_64	NOTE	Jan 24 2025
R-4.5-linux-x86_64	NOTE	Jan 24 2025
R-4.4-win-x86_64	NOTE	Jan 24 2025
R-4.4-mac-x86_64	NOTE	Jan 24 2025
R-4.4-mac-aarch64	NOTE	Jan 24 2025
R-4.3-win-x86_64	NOTE	Jan 24 2025
R-4.3-mac-x86_64	NOTE	Jan 24 2025
R-4.3-mac-aarch64	NOTE	Jan 24 2025

Exports:cluster_irr dco detect_communities get_ag_summary get_beta_violins get_clustirr_clust get_clustirr_inputs get_graph get_honeycombs get_joint_graph plot_graph

Dependencies:abind backports base64enc BH blaster bslib cachem callr checkmate cli codetools colorspace cpp11 desc digest distributional dplyr evaluate fansi farver fastmap fontawesome fs future future.apply generics ggforce ggplot2 globals glue gridExtra gtable highr htmltools htmlwidgets igraph inline isoband jquerylib jsonlite knitr labeling lattice lifecycle listenv loo magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme numDeriv parallelly pillar pkgbuild pkgconfig plyr polyclip posterior processx ps purrr QuickJSR R6 rappdirs RColorBrewer Rcpp RcppEigen RcppParallel reshape2 rlang rmarkdown rstan rstantools sass scales StanHeaders stringdist stringi stringr systemfonts tensorA tibble tidyr tidyselect tinytex tweenr utf8 vctrs viridisLite visNetwork withr xfun yaml

Analysis of T and B cell receptor repertoires with ClustIRR

Rendered fromUser_manual.Rmdusingknitr::rmarkdownon Jan 24 2025.

Last update: 2025-01-09
Started: 2023-05-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BLOSUM62 matrix	BLOSUM62
Mock data set of complementarity determining region 3 (CDR3) sequences and variable (V) and joining (J) genes from the alpha and beta chains of 10,000 T cell receptors.	CDR3ab
clust_irr class	class:clust_irr clust_irr clust_irr-class get_clustirr_clust get_clustirr_clust,clust_irr-method get_clustirr_inputs get_clustirr_inputs,clust_irr-method
Clustering of immune receptor repertoires (IRRs)	cluster_irr
Model-based differential community occupancy (DCO) analysis	dco
Graph-based community detection (GCD)	detect_communities
Estimate the number of antigen-specific T-cells in selected communities	get_ag_summary
Generate beta violin plot: visualize distribution of beta coefficient means for communities in immune receptor repertoires	get_beta_violins
Get 'igraph' object from 'clust_irr' object	get_graph
Generate honycomb plot: visualize community occupancy of pairs of immune receptor repertoires	get_honeycombs
Create joint 'igraph' object from multiple 'clust_irr' objects	get_joint_graph
CDR3 sequences and their matching epitopes obtained from McPAS-TCR	mcpas
Plot ClustIRR graph	plot_graph
CDR3 sequences and their matching epitopes obtained from TCR3d	tcr3d
CDR3 sequences and their matching epitopes obtained from VDJdb	vdjdb