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:
immunarch_0.9.1.tar.gz
immunarch_0.9.1.zip(r-4.5)immunarch_0.9.1.zip(r-4.4)immunarch_0.9.1.zip(r-4.3)
immunarch_0.9.1.tgz(r-4.5-x86_64)immunarch_0.9.1.tgz(r-4.5-arm64)immunarch_0.9.1.tgz(r-4.4-x86_64)immunarch_0.9.1.tgz(r-4.4-arm64)immunarch_0.9.1.tgz(r-4.3-x86_64)immunarch_0.9.1.tgz(r-4.3-arm64)
immunarch_0.9.1.tar.gz(r-4.5-noble)immunarch_0.9.1.tar.gz(r-4.4-noble)
immunarch_0.9.1.tgz(r-4.4-emscripten)immunarch_0.9.1.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/immunomind/immunarch/issues
Pkgdown site:https://immunarch.com
airr-analysisb-cell-receptorbcrbcr-repertoirebioinformaticsigig-repertoireimmune-repertoireimmune-repertoire-analysisimmune-repertoire-dataimmunoglobulinimmunoinformaticsimmunologyrep-seqrepertoire-analysissingle-cellsingle-cell-analysist-cell-receptortcrtcr-repertoirecpp
Last updated 1 years agofrom:0b6544a101. Checks:8 OK, 4 NOTE. Indexed: yes.
Target | Result | Latest binary |
---|---|---|
Doc / Vignettes | OK | Mar 20 2025 |
R-4.5-win-x86_64 | NOTE | Mar 20 2025 |
R-4.5-mac-x86_64 | NOTE | Mar 20 2025 |
R-4.5-mac-aarch64 | NOTE | Mar 20 2025 |
R-4.5-linux-x86_64 | NOTE | Mar 20 2025 |
R-4.4-win-x86_64 | OK | Mar 20 2025 |
R-4.4-mac-x86_64 | OK | Mar 20 2025 |
R-4.4-mac-aarch64 | OK | Mar 20 2025 |
R-4.4-linux-x86_64 | OK | Mar 20 2025 |
R-4.3-win-x86_64 | OK | Mar 20 2025 |
R-4.3-mac-x86_64 | OK | Mar 20 2025 |
R-4.3-mac-aarch64 | OK | Mar 20 2025 |
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.tabledendextendDEoptimRDerivdigestdiptestdoBydoParalleldplyrDTdtplyrellipseemmeansestimabilityevaluatefactoextraFactoMineRfansifarverfastmapfastmatchflashClustflexmixfontawesomeforeachFormulafpcfsgenericsggalluvialggforceggplot2ggpubrggraphggrepelggsciggseqlogoggsignifGlobalOptionsgluegraphlayoutsgridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvigraphisobanditeratorsjquerylibjsonlitekernlabknitrlabelinglaterlatticelazyevalleapslifecyclelme4magrittrMASSMatrixMatrixModelsmclustmemoisemgcvmicrobenchmarkmimeminqamodelrmodeltoolsmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivpatchworkpbkrtestphangornpheatmappillarpkgconfigplyrpolyclippolynomprabclusprettyunitsprogresspromisespurrrquadprogquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadxlreformulasrematchreshape2rlangrlistrmarkdownrobustbaserstatixRtsnesassscalesscatterplot3dshapeshinyshinythemessourcetoolsSparseMstringdiststringistringrsurvivalsystemfontstibbletidygraphtidyrtidyselecttinytextweenrtzdbUpSetRutf8uuidvctrsviridisviridisLitevroomwithrxfunXMLxtableyaml