Package: immunarch 0.9.1

Vadim I. Nazarov

immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.

Authors:Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Siarhei Fiadziushchanka [aut], Eugene Rumynskiy [aut], Aleksandr A. Popov [aut], Ivan Balashov [aut], Maria Samokhina [aut], Anna Lorenc [ctb], Daniel J. Moore [ctb], Victor Greiff [ctb], ImmunoMind [cph, fnd]

immunarch_0.9.1.tar.gz
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immunarch.pdf |immunarch.html✨
immunarch/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • AA_PROP - Tables with amino acid properties
  • ATCHLEY - Tables with amino acid properties
  • GENE_SEGMENTS - Gene segments table
  • KIDERA - Tables with amino acid properties
  • bcrdata - BCR dataset
  • immdata - Single chain immune repertoire dataset
  • scdata - Paired chain immune repertoire dataset

On CRAN:

airr-analysisb-cell-receptorbcrbcr-repertoirebioinformaticsigig-repertoireimmune-repertoireimmune-repertoire-analysisimmune-repertoire-dataimmunoglobulinimmunoinformaticsimmunologyrep-seqrepertoire-analysissingle-cellsingle-cell-analysist-cell-receptortcrtcr-repertoire

9.48 score 311 stars 200 scripts 798 downloads 6 mentions 71 exports 172 dependencies

Last updated 8 months agofrom:0b6544a101. Checks:OK: 7 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64NOTENov 20 2024
R-4.5-linux-x86_64NOTENov 20 2024
R-4.4-win-x86_64OKNov 20 2024
R-4.4-mac-x86_64OKNov 20 2024
R-4.4-mac-aarch64OKNov 20 2024
R-4.3-win-x86_64OKNov 20 2024
R-4.3-mac-x86_64OKNov 20 2024
R-4.3-mac-aarch64OKNov 20 2024

Exports:apply_asymmapply_symmbunch_translatecodingcross_entropydbAnnotatedbLoadentropyexcludefixVisgene_statsgeneUsagegeneUsageAnalysisget_genesgetKmersimmunr_dbscanimmunr_hclustimmunr_kmeansimmunr_mdsimmunr_pcaimmunr_tsneinc_overlapincludeinframesintervaljs_divkl_divkmer_profilelessthanmorethannoncodingoutofframespublic_matrixpublicRepertoirepublicRepertoireApplypublicRepertoireFilterpubReppubRepApplypubRepFilterpubRepStatisticsrepAlignLineagerepClonalFamilyrepClonalityrepDiversityrepExplorerepFilterrepGermlinerepLoadrepOverlaprepOverlapAnalysisrepSamplerepSaverepSomaticHypermutationselect_barcodesselect_clustersseqClusterseqDistspectratypesplit_to_kmerstoptrackClonotypesvisvis_barvis_boxvis_circosvis_heatmapvis_heatmap2vis_histvis_immunr_kmer_profile_mainvis_seqlogovis_textlogo

Dependencies:abindairrapebackportsbase64encbitbit64bootbroombslibcachemcarcarDatacellrangercirclizeclassclicliprclustercodetoolscolorspacecommonmarkcorrplotcowplotcpp11crayoncrosstalkdata.tabledendextendDEoptimRDerivdigestdiptestdoBydoParalleldplyrDTdtplyrellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapfastmatchflashClustflexmixfontawesomeforeachFormulafpcfsgenericsggalluvialggforceggplot2ggpubrggraphggrepelggsciggseqlogoggsignifGlobalOptionsgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvigraphisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmclustmemoisemgcvmicrobenchmarkmimeminqamodelrmodeltoolsmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpatchworkpbkrtestphangornpheatmappillarpkgconfigplyrpolyclippolynomprabclusprettyunitsprogresspromisespurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadrreadxlrematchreshape2rlangrlistrmarkdownrobustbaserstatixRtsnesassscalesscatterplot3dshapeshinyshinythemessourcetoolsSparseMstringdiststringistringrsurvivalsystemfontstibbletidygraphtidyrtidyselecttinytextweenrtzdbUpSetRutf8uuidvctrsviridisviridisLitevroomwithrxfunXMLxtableyaml

Introduction to immunarch

ImmunoMind – improving design of T-cell therapies using multi-omics and AI. Research and biopharma partnerships, more details: immunomind.com

Rendered fromv1_introduction.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-03-19
Started: 2020-05-13

Data loading

ImmunoMind – improving design of T-cell therapies using multi-omics and AI. Research and biopharma partnerships, more details: immunomind.com

Rendered fromv2_data.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-03-19
Started: 2020-05-13

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
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 such as VDJDB and MCPASdbAnnotate
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
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
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
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
Calculates number of mutations against the germline for each clonotyperepSomaticHypermutation
Paired chain immune repertoire datasetscdata
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