c(
person("Vadim I.", "Nazarov", , "support@immunomind.io", c("aut", "cre")),
person("Vasily O.", "Tsvetkov", , role = "aut"),
person("Eugene", "Rumynskiy", , role = "aut"),
person("Aleksandr A.", "Popov", , role = "aut"),
person("Ivan", "Balashov", , role = "aut"),
person("Maria", "Volobueva", , role = "aut"),
person("Anna", "Lorenc", , role = "ctb"),
person("Daniel J.", "Moore", , role = "ctb"),
person("Victor", "Greiff", , role = "ctb"),
person("ImmunoMind", role = c("cph", "fnd"))
)
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
Vadim I. Nazarov [aut, cre],
Vasily O. Tsvetkov [aut],
Eugene Rumynskiy [aut],
Aleksandr A. Popov [aut],
Ivan Balashov [aut],
Maria Volobueva [aut],
Anna Lorenc [ctb],
Daniel J. Moore [ctb],
Victor Greiff [ctb],
ImmunoMind [cph, fnd]

c(
person("Vadim I.", "Nazarov", , "support@immunomind.io", c("aut", "cre")),
person("Vasily O.", "Tsvetkov", , role = "aut"),
person("Eugene", "Rumynskiy", , role = "aut"),
person("Aleksandr A.", "Popov", , role = "aut"),
person("Ivan", "Balashov", , role = "aut"),
person("Maria", "Samokhina", , role = "aut"),
person("Anna", "Lorenc", , role = "ctb"),
person("Daniel J.", "Moore", , role = "ctb"),
person("Victor", "Greiff", , role = "ctb"),
person("ImmunoMind", role = c("cph", "fnd"))
)
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>.
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
Vadim I. Nazarov [aut, cre],
Vasily O. Tsvetkov [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]