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

A comprehensive framework for bioinformatics 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: 0.6.4
Depends: R (≥ 3.5.0), ggplot2 (≥ 3.1.0), dplyr (≥ 0.8.0), dtplyr (≥ 1.0.0), data.table (≥ 1.12.6), gridExtra (≥ 2.2.1)
Imports: pheatmap (≥ 1.0.12), ggrepel (≥ 0.8.0), reshape2 (≥ 1.4.2), factoextra (≥ 1.0.4), fpc, circlize, MASS (≥ 7.3), Rtsne (≥ 0.15), readr (≥ 1.3.1), readxl (≥ 1.3.1), shiny (≥ 1.4.0), shinythemes, treemap, airr, ggseqlogo, UpSetR (≥ 1.4.0), stringr (≥ 1.4.0), ggalluvial (≥ 0.10.0), Rcpp (≥ 1.0), magrittr, tibble (≥ 2.0), methods, scales, ggpubr (≥ 0.2), rlang (≥ 0.4), plyr, dbplyr (≥ 1.4.0)
LinkingTo: Rcpp
Suggests: knitr (≥ 1.8), roxygen2 (≥ 3.0.0), testthat (≥ 2.1.0), pkgdown (≥ 0.1.0), assertthat
Published: 2020-05-13
Author: Vadim I. Nazarov [aut, cre], Vasily O. Tsvetkov [aut], Eugene Rumynskiy [aut], Anna Lorenc [aut], Daniel J. Moore [aut], Victor Greiff [aut], ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <vdm.nazarov at gmail.com>
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

Downloads:

Reference manual: immunarch.pdf
Vignettes: Introduction to immunarch
Working with data in immunarch
Basic analysis and clonality
Package source: immunarch_0.6.4.tar.gz
Windows binaries: r-devel: immunarch_0.6.4.zip, r-release: immunarch_0.6.4.zip, r-oldrel: immunarch_0.6.4.zip
macOS binaries: r-release: immunarch_0.6.4.tgz, r-oldrel: immunarch_0.6.4.tgz

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