Package: ClustIRR 1.11.1

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_1.11.1.tar.gz
ClustIRR_1.11.1.zip(r-4.7)ClustIRR_1.11.1.zip(r-4.6)ClustIRR_1.11.1.zip(r-4.5)
ClustIRR_1.11.1.tgz(r-4.6-x86_64)ClustIRR_1.11.1.tgz(r-4.6-arm64)ClustIRR_1.11.1.tgz(r-4.5-x86_64)ClustIRR_1.11.1.tgz(r-4.5-arm64)
ClustIRR_1.11.1.tar.gz(r-4.7-arm64)ClustIRR_1.11.1.tar.gz(r-4.7-x86_64)ClustIRR_1.11.1.tar.gz(r-4.6-arm64)ClustIRR_1.11.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ClustIRR/json (API)

# 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
  • D_CMV_FLU - Processed single-cell TCR and gene expression dataset of antigen stimulated T cells
  • D1 - Synthetic dataset 'D1' with three TCRalphabeta repertoires
  • D2 - Synthetic dataset 'D2' with six TCRalphabeta repertoires
  • 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-1.11.0(bioc 3.24)ClustIRR-1.10.0(bioc 3.23)

clusteringimmunooncologysinglecellsoftwareclassificationbayesianbiomedicalinformaticsmathematicalbiologyb-cell-receptorbioinformaticsimmunoinformaticsimmunologyquantitative-methodsrep-seqrepertoire-analysist-cell-receptorcpp

5.08 score 5 stars 5 scripts 19 exports 114 dependencies

Last updated from:a562a197b5. Checks:1 WARNING, 12 ERROR, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING309
linux-devel-arm64ERROR359
linux-devel-x86_64ERROR421
source / vignettesERROR457
linux-release-arm64ERROR375
linux-release-x86_64ERROR386
macos-release-arm64ERROR356
macos-release-x86_64ERROR506
macos-oldrel-arm64ERROR221
macos-oldrel-x86_64ERROR626
windows-develERROR427
windows-releaseERROR383
windows-oldrelERROR446
wasm-releaseFAIL211

Exports:clustirrdcodecode_all_communitiesdecode_communitydetect_communitiesget_ag_gene_hitsget_ag_species_hitsget_beta_cprob_agget_beta_violin_agget_cdr3_motifsget_clustirr_clustget_clustirr_inputsget_community_feature_purityget_community_feature_statsget_cosine_similarityget_honeycombsget_nradsplot_graphsave_interactive_graph

Dependencies:abindaskpassbackportsbase64encBHBiocFileCacheBiocGenericsBiostringsbitbit64blobbslibcachemcallrcheckmateclicpp11crayoncurlDBIdbplyrdescdigestdistributionaldplyrevaluatefarverfastmapfilelockfontawesomefsgenericsggforceggplot2ggseqlogogluegridExtragtablehighrhtmltoolshtmlwidgetshttr2igraphinlineIRangesisobandjquerylibjsonliteknitrlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmemoisemimemsaMultipleAlignmentnumDerivopensslotelpillarpkgbuildpkgconfigplyrpolyclipposteriorprocessxpspurrrQuickJSRR6RADanalysisrappdirsrBLASTRColorBrewerRcppRcppEigenRcppParallelreshape2rlangrmarkdownRSQLiterstanrstantoolsS4VectorsS7sassscalesSeqinfosfsmiscStanHeadersstringdiststringistringrsyssystemfontstensorAtibbletidyrtidyselecttinytextweenrutf8vctrsviridisLitevisNetworkwithrxfunXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
BLOSUM62 matrixBLOSUM62
clust_irr classclass: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)clustirr
Processed single-cell TCR and gene expression dataset of antigen stimulated T cellsD_CMV_FLU
Synthetic dataset 'D1' with three TCRalphabeta repertoiresD1
Synthetic dataset 'D2' with six TCRalphabeta repertoiresD2
Model-based differential community occupancy (DCO) analysisdco
Decode all graph communitiesdecode_all_communities
Decode graph communitiesdecode_community
Graph-based community detection (GCD)detect_communities
Annotate antigen gene hits in node summaryget_ag_gene_hits
Annotate antigen species hits in node summaryget_ag_species_hits
Visualize cumulative probability of beta means for antigen-specific communitiesget_beta_cprob_ag
Visualize distribution of beta means in each repertoire as violin plotsget_beta_violin_ag
Generate CDR3 motif for communitiesget_cdr3_motifs
Compute community purity with respect to a node featureget_community_feature_purity
Compute descriptive statistics of a community node featureget_community_feature_stats
Compute and Visualize Cosine Similarity (CS)get_cosine_similarity
Generate honycomb plot: visualize community occupancy of pairs of immune receptor repertoiresget_honeycombs
Compute Normalized Rank Abundance Distributions (NRADs)get_nrads
CDR3 sequences and their matching epitopes obtained from McPAS-TCRmcpas
Plot ClustIRR graphplot_graph
Save interactive ClustIRR graphsave_interactive_graph
CDR3 sequences and their matching epitopes obtained from TCR3dtcr3d
CDR3 sequences and their matching epitopes obtained from VDJdbvdjdb