Package: immunarch 0.10.3.9002

Vadim I. Nazarov

immunarch: Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design in R

A comprehensive analytics framework for building reproducible pipelines on T-cell and B-cell immune receptor repertoire data. Delivers multi-modal immune profiling (bulk, single-cell, CITE-seq/AbSeq, spatial, immunogenicity data), feature engineering (ML-ready feature tables and matrices), and biomarker discovery workflows (cohort comparisons, longitudinal tracking, repertoire similarity, enrichment). Provides a user-friendly interface to widely used AIRR methods — clonality/diversity, V(D)J usage, similarity, annotation, tracking, and many more. Think Scanpy or Seurat, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or VDJ sequencing data. A successor to our previously published "tcR" R package (Nazarov 2015).

Authors:Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Aleksandr A. Popov [aut], Ivan Balashov [aut]

immunarch_0.10.3.9002.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
immunarch/json (API)
NEWS

# Install 'immunarch' in R:
install.packages('immunarch', repos = c('https://immunomind.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immunomind/immunarch/issues

Pkgdown/docs site:https://immunarch.com

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

airrbioinformaticsdata-scienceimmune-repertoireimmunomicsimmunotherapyvaccinecpp

10.18 score 339 stars 313 scripts 878 downloads 6 mentions 89 exports 78 dependencies

Last updated from:274afb2188. Checks:13 OK. Indexed: yes.

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linux-devel-x86_64OK288
source / vignettesOK320
linux-release-arm64OK254
linux-release-x86_64OK285
macos-release-arm64OK223
macos-release-x86_64OK346
macos-oldrel-arm64OK234
macos-oldrel-x86_64OK388
windows-develOK225
windows-releaseOK226
windows-oldrelOK227
wasm-releaseOK186

Exports:airr_clonality_lineairr_clonality_propairr_clonality_rankairr_desc_chainsairr_desc_genesairr_desc_lengthsairr_diversity_chao1airr_diversity_dxxairr_diversity_hillairr_diversity_indexairr_diversity_pielouairr_diversity_shannonannotate_clonality_propannotate_clonality_rankapply_asymmapply_symmbunch_translatecodingcross_entropydbAnnotatedbLoadentropyexcludefixVisgene_statsgeneUsagegeneUsageAnalysisget_genesget_immunarch_newsgetKmersimmunr_dbscanimmunr_hclustimmunr_kmeansimmunr_mdsimmunr_pcaimmunr_tsneinc_overlapincludeinframesintervaljs_divkl_divkmer_profilelessthanlist_immunarch_newsmorethannoncodingoutofframespublic_matrixpublicRepertoirepublicRepertoireApplypublicRepertoireFilterpubReppubRepApplypubRepFilterpubRepStatisticsrepAlignLineagerepClonalFamilyrepClonalityrepDiversityrepExplorerepFilterrepGermlinerepLoadrepOverlaprepOverlapAnalysisrepSamplerepSaverepsim_intersectionrepsim_jaccardrepSomaticHypermutationselect_barcodesselect_clustersseqClusterseqDistspectratypesplit_to_kmerstoptrackClonotypesvisvis_barvis_boxvis_circosvis_heatmapvis_heatmap2vis_histvis_immunr_kmer_profile_mainvis_seqlogovis_textlogo

Dependencies:airrapebackportsbitbit64blobcachemcheckmatecirclizeclicliprcodetoolscollectionscolorspacecpp11crayondata.tableDBIdbplyrdigestdoParalleldplyrdtplyrduckdbduckplyrfarverfastmapforeachgenericsggplot2ggsciggthemesGlobalOptionsgluegtablehmsimmundataisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmemoisenlmepatchworkpheatmappillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcppreadrreshape2rlangrlistS7scalesshapestringdiststringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXMLyaml

Immunarch overview

Rendered fromimmunarch.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-10-14
Started: 2025-10-10

Limit the number of threads used by immunarch

Rendered fromimmunarch_threads.Rmdusingknitr::rmarkdownon May 21 2026.

Last update: 2025-10-14
Started: 2025-10-14

Readme and manuals

Help Manual

Help pageTopics
Get a column's name using the input alias.quant_column_choice
Tables with amino acid propertiesAA_PROP aa_prop aa_properties ATCHLEY atchley KIDERA kidera properties
Amino acid / codon tableAA_TABLE aa_table AA_TABLE_REVERSED
Add a new class attributeadd_class
Clonality - receptor overabundance statistics for immune repertoiresairr_clonality airr_clonality_line airr_clonality_prop airr_clonality_rank
Compute key immune repertoire statisticsairr_desc airr_desc_chains airr_desc_genes airr_desc_lengths
Diversity - estimating the heterogeneity of immune repertoiresairr_diversity airr_diversity_chao1 airr_diversity_dxx airr_diversity_hill airr_diversity_index airr_diversity_pielou airr_diversity_shannon
Annotate clonality - per-receptor labels for overabundanceannotate_clonality annotate_clonality_prop annotate_clonality_rank
Apply function to each pair of data frames from a list.apply_asymm apply_symm
BCR datasetbcrdata
Nucleotide to amino acid sequence translationbunch_translate translate_bunch
Check and normalise distributionscheck_distribution
Filter out coding and non-coding clonotype sequencescoding inframes noncoding outofframes
Annotate clonotypes in immune repertoires using clonotype databases (e.g., VDJDB, McPAS)dbAnnotate
Load clonotype databases such as VDJDB and McPAS into the R workspacedbLoad
Information measurescross_entropy entropy js_div kl_div
Manipulate ggplot plots and create publication-ready plotsfixVis
Gene segments tablegenes GENE_SEGMENTS gene_segments segments
WIPgene_stats
Main function for estimation of V-gene and J-gene statisticsgeneUsage get_aliases get_genes
Post-analysis of V-gene and J-gene statistics: PCA, clustering, etc.geneUsageAnalysis
Get the Latest immunarch Updateget_immunarch_news
Calculate the k-mer statistics of immune repertoiresget.kmers getKmers makeKmerTable
Get a character vector of samples' groups from the input metadata filegroup_from_metadata
Check for the specific classhas_class
Single chain immune repertoire datasetimmdata
Get a list of package updatesimmunarch_v1_updates
Specification of the data format used by immunarch dataframesimmunarch_data_format immunr_data_format
Clustering of objects or distance matricesimmunr_dbscan immunr_hclust immunr_kmeans
Dimensionality reductionimmunr_mds immunr_pca immunr_tsne
Incremental counting of repertoire similarityinc_overlap
List Available immunarch Updateslist_immunarch_news
Copy the upper matrix triangle to the lower onematrixdiagcopy
Get a matrix with public clonotype frequenciespublic_matrix
Create a repertoire of public clonotypespublicRepertoire pubRep
Apply transformations to public repertoirespublicRepertoireApply pubRepApply
Filter out clonotypes from public repertoirespublicRepertoireFilter pubRepFilter
Statistics of number of public clonotypes for each possible combinations of repertoirespubRepStatistics
Aligns all sequences incliding germline within each clonal lineage within each clusterrepAlignLineage
Builds a phylogenetic tree using the sequences of a clonal lineagerepClonalFamily
Clonality analysis of immune repertoiresclonal.prop clonality clonal_proportion clonal_space_homeostasis rare_proportion repClonality top_proportion
The main function for immune repertoire diversity estimationchao1 diversity_eco gini_coef gini_simpson hill_numbers inverse_simpson rarefaction repDiversity
Main function for exploratory data analysis: compute the distribution of lengths, clones, etc.repExplore
Main function for data filteringexclude include interval lessthan morethan repFilter
Creates germlines for clonal lineagesrepGermline
Load immune repertoire files into the R workspacerepLoad
Main function for public clonotype statistics calculationsrepOverlap
Post-analysis of public clonotype statistics: PCA, clustering, etc.repOverlapAnalysis
Downsampling and resampling of immune repertoiresrepSample
Save immune repertoires to the diskrepSave
Public indices - pairwise repertoire overlaprepsim repsim_intersection repsim_jaccard
Calculates number of mutations against the germline for each clonotyperepSomaticHypermutation
Select specific clonotypes using barcodes from single-cell metadataselect_barcodes
Split the immune repertoire data to clusters from single-cell barcodesselect_clusters
Function for assigning clusters based on sequences similarityseqCluster
Function for computing distance for sequencesseqDist
Set and update progress barsadd_pb set_pb
Immune repertoire spectratypingspectratype
Analysis immune repertoire kmer statistics: sequence profiles, etc.kmer_profile split_to_kmers
Return a column's nameprocess_col_argument switch_type
Get the N most abundant clonotypestop
Track clonotypes across time and data pointstrackClonotypes
One function to visualise them allvis
Bar plotsvis_bar
Flexible box-plots for visualisation of distributionsvis_box
Visualisation of matrices using circos plotsvis_circos
Visualisation of matrices and data frames using ggplo2-based heatmapsvis_heatmap
Visualisation of matrices using pheatmap-based heatmapsvis_heatmap2
Visualisation of distributions using histogramsvis_hist
Visualise kmer profilesvis_immunr_kmer_profile_main
Visualisation of public clonotypesvis_public_clonotypes
Public repertoire visualisationvis_public_frequencies
Sequence logo plots for amino acid profiles.vis_seqlogo vis_textlogo
Visualise clonal family tree: wrapper for calling on the entire repClonalFamily outputvis.clonal_family
Visualise clonal family treevis.clonal_family_tree
Visualise diversity.vis.immunr_chao1 vis.immunr_div vis.immunr_dxx vis.immunr_ginisimp vis.immunr_hill vis.immunr_invsimp vis.immunr_rarefaction
Visualise results of the clonality analysisvis.immunr_clonal_prop vis.immunr_homeo vis.immunr_tail_prop vis.immunr_top_prop
Visualise clonotype dynamicsvis.immunr_dynamics
Visualise results of the exploratory analysisvis.immunr_exp_clones vis.immunr_exp_count vis.immunr_exp_len vis.immunr_exp_vol
Histograms and boxplots (general case / gene usage)vis.immunr_gene_usage
Visualisation of hierarchical clusteringvis.immunr_hclust
Visualise incremental overlapsvis.immunr_inc_overlap
Visualisation of K-means and DBSCAN clusteringvis.immunr_dbscan vis.immunr_kmeans
Most frequent kmers visualisation.vis.immunr_kmer_table
PCA / MDS / tSNE visualisation (mainly overlap / gene usage)vis.immunr_mds vis.immunr_pca vis.immunr_tsne
Repertoire overlap and gene usage visualisationsvis.immunr_gu_matrix vis.immunr_ov_matrix
Public repertoire visualisationvis.immunr_public_repertoire
Visualise sharing of clonotypes among samplesvis.immunr_public_statistics
Handler for .nofail argument of pipeline steps that prevents examples from crashing on computers where certain dependencies are not installedvis.step_failure_ignored