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). It 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: 0.6.7
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, dbplyr (≥ 1.4.0), jsonlite, readr, stringr, tibble, tidyselect, purrr
LinkingTo: Rcpp
Suggests: knitr (≥ 1.8), roxygen2 (≥ 3.0.0), testthat (≥ 2.1.0), pkgdown (≥ 0.1.0), assertthat, rmarkdown
Published: 2021-10-29
Author: Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Eugene Rumynskiy [aut], Aleksandr A. Popov [aut], Ivan Balashov [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: AGPL-3
URL: https://immunarch.com/, https://github.com/immunomind/immunarch
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: immunarch results

Documentation:

Reference manual: immunarch.pdf
Vignettes: Introduction to immunarch
Working with data in immunarch

Downloads:

Package source: immunarch_0.6.7.tar.gz
Windows binaries: r-devel: immunarch_0.6.7.zip, r-devel-UCRT: immunarch_0.6.7.zip, r-release: immunarch_0.6.7.zip, r-oldrel: immunarch_0.6.7.zip
macOS binaries: r-release (arm64): immunarch_0.6.7.tgz, r-release (x86_64): immunarch_0.6.7.tgz, r-oldrel: immunarch_0.6.7.tgz
Old sources: immunarch archive

Linking:

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