Package: ClustIRR 1.3.16

Simo Kitanovski

ClustIRR: Clustering of immune receptor repertoires

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.

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

ClustIRR_1.3.16.tar.gz
ClustIRR_1.3.16.zip(r-4.5)ClustIRR_1.3.16.zip(r-4.4)ClustIRR_1.3.16.zip(r-4.3)
ClustIRR_1.3.16.tgz(r-4.4-any)ClustIRR_1.3.16.tgz(r-4.3-any)
ClustIRR_1.3.16.tar.gz(r-4.5-noble)ClustIRR_1.3.16.tar.gz(r-4.4-noble)
ClustIRR_1.3.16.tgz(r-4.4-emscripten)ClustIRR_1.3.16.tgz(r-4.3-emscripten)
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

Datasets:

CDR3ab - Mock data set of complementarity determining region 3 (CDR3) sequences 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-1.3.8(bioc 3.20)ClustIRR-1.2.0(bioc 3.19)

bioconductor-package

6 exports 2.38 score 61 dependencies

Last updated 6 days agofrom:2d05af467c

Exports:cluster_irr get_clustirr_clust get_clustirr_inputs get_graph get_joint_graph plot_graph

Dependencies:askpass base64enc BH BiocGenerics BiocParallel Biostrings blaster bslib cachem cli codetools cpp11 crayon curl digest evaluate fastmap fontawesome formatR fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData glue highr htmltools htmlwidgets httr igraph IRanges jquerylib jsonlite knitr lambda.r lattice lifecycle magrittr Matrix memoise mime openssl pkgconfig R6 rappdirs Rcpp rlang rmarkdown S4Vectors sass snow stringdist sys tinytex UCSC.utils vctrs visNetwork xfun XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mock data set of complementarity determining region 3 (CDR3) sequences 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	cluster_irr
Get graph structure from 'clust_irr' object	get_graph
Joins two graphs obtained from two or more '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