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>.
Version: 0.9.1 Depends: R (≥ 4.0.0), ggplot2 (≥ 3.1.0), dplyr (≥ 0.8.0), dtplyr (≥ 1.0.0), data.table (≥ 1.12.6), patchwork Imports: factoextra (≥ 1.0.4), fpc, UpSetR (≥ 1.4.0), pheatmap (≥ 1.0.12), ggrepel (≥ 0.8.0), reshape2 (≥ 1.4.2), circlize, MASS (≥ 7.3), Rtsne (≥ 0.15), readxl (≥ 1.3.1), shiny (≥ 1.4.0), shinythemes, airr, ggseqlogo, ggalluvial (≥ 0.10.0), Rcpp (≥ 1.0), magrittr, methods, scales, ggpubr (≥ 0.2), rlang (≥ 0.4), plyr, purrr, stringdist, jsonlite, readr, stringr, tibble, tidyselect, tidyr, igraph, ape, doParallel, rlist, utils, glue, phangorn, uuid, stringi, ggraph LinkingTo: Rcpp Suggests: knitr (≥ 1.8), roxygen2 (≥ 3.0.0), testthat (≥ 2.1.0), pkgdown (≥ 0.1.0), assertthat, rmarkdown Published: 2024-03-18 DOI: 10.32614/CRAN.package.immunarch Author: 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] Maintainer: Vadim I. Nazarov <support at immunomind.io> Contact: support@immunomind.io BugReports: https://github.com/immunomind/immunarch/issues License: Apache License (== 2.0) URL: https://immunarch.com/, https://github.com/immunomind/immunarch NeedsCompilation: yes Materials: README NEWS In views: Omics CRAN checks: immunarch results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=immunarch to link to this page.
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