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

Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program. See Robitzsch and
Steinfeld (2018) for a description of the functionality
of the package.
CDM (>= 6.0-101), coda, graphics, MASS, methods, psychotools,
Rcpp, sirt (>= 2.4-9), stats, TAM

Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program. See Robitzsch and
Steinfeld (2018) for a description of the functionality
of the package.
See Wang, Su & Qiu (2014; <doi:10.1111/jedm.12045>)
for an overview of modeling alternatives.

Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program. See Robitzsch and
Steinfeld (2018) for a description of the functionality
of the package.
See Wang, Su and Qiu (2014; <doi:10.1111/jedm.12045>)
for an overview of modeling alternatives.
CDM, coda, graphics, methods, psychotools, Rcpp, sirt, stats,
TAM

Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
c(
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"))
)
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>.
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)
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]