to the commercial FACETS program. See Robitzsch and
Steinfeld (2018) for a description of the functionality
Imports: CDM (>= 6.0-101), coda, graphics, MASS, methods, psychotools,

for an overview of modeling alternatives.

Imports: CDM, coda, graphics, methods, psychotools, Rcpp, sirt, stats,

Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
person("Vadim I.", "Nazarov", , "vdm.nazarov@gmail.com", c("aut", "cre")),
person("Vasily O.", "Tsvetkov", , role = "aut"),
person("Eugene", "Rumynskiy", , role = "aut"),
person("Anna", "Lorenc", , role = "aut"),
person("Daniel J.", "Moore", , role = "aut"),
person("Victor", "Greiff", , role = "aut"),
person("ImmunoMind", role = c("cph", "fnd"))
Description: 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>.
factoextra (>= 1.0.4), fpc, circlize, MASS (>= 7.3), Rtsne (>=
shinythemes, treemap, airr, ggseqlogo, UpSetR (>= 1.4.0),
magrittr, tibble (>= 2.0), methods, scales, ggpubr (>= 0.2),
Maintainer: Vadim I. Nazarov <vdm.nazarov@gmail.com>

person("Anna", "Lorenc", , role = "ctb"),
person("Daniel J.", "Moore", , role = "ctb"),
person("Victor", "Greiff", , role = "ctb"),
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
Imports: factoextra (>= 1.0.4), fpc, UpSetR (>= 1.4.0), pheatmap (>=
1.3.1), shiny (>= 1.4.0), shinythemes, airr, ggseqlogo, stringr
tibble (>= 2.0), methods, scales, ggpubr (>= 0.2), rlang (>=