Package: piglet
Title: Program for Inferring Immunoglobulin Allele Similarity Clusters
        and Genotypes
Version: 1.2.0
Authors@R: c(person("Ayelet", "Peres", role=c("aut","cre"),
                    email="ayelet.peres@yale.edu"),
            person("William", "Lees", role=c("aut"),
                    email="william@lees.org.uk"),
             person("Gur", "Yaari", role=c("aut","cph"),
                    email="gur.yaari@yale.edu"))
Author: Ayelet Peres [aut, cre],
  William Lees [aut],
  Gur Yaari [aut, cph]
Maintainer: Ayelet Peres <ayelet.peres@yale.edu>
Description: Improves genotype inference and downstream Adaptive Immune Receptor Repertoire Sequence data analysis. Inference of allele similarity clusters, an alternative naming scheme and genotype inference for immunoglobulin heavy chain repertoires.
             The main tools are allele similarity clusters, and allele based genotype. The first tool is designed to reduce the ambiguity within the immunoglobulin heavy chain V alleles. The ambiguity is caused by duplicated or similar alleles which are shared among different genes.
             The second tool is an allele based genotype, that determined the presence of an allele based on a threshold derived from a naive population. See Peres et al. (2023) <doi:10.1093/nar/gkad603>.
License: CC BY-SA 4.0
Encoding: UTF-8
Depends: R (>= 3.5.0)
LinkingTo: Rcpp
SystemRequirements: GNU make
Imports: Biostrings (>= 2.62.0), DECIPHER (>= 2.22.0), alakazam (>=
        1.2.0), dendextend (>= 1.9.0), data.table (>= 1.12.2), tigger
        (>= 1.0.0), methods (>= 3.4.4), rlang (>= 0.4.0), zen4R (>=
        0.7), RColorBrewer (>= 1.1.2), ggplot2 (>= 3.3.6), circlize (>=
        0.4.15), R6 (>= 2.5.1), jsonlite (>= 1.8.3), Rcpp (>= 0.11.0),
        magrittr, igraph (>= 1.3.0), stringdist (>= 0.9.0), cluster (>=
        2.1.0), ape (>= 5.0)
Suggests: knitr, rmarkdown, tidyr, htmltools, stringi, bookdown,
        ComplexHeatmap, dplyr, ggtree (>= 3.0.0), testthat (>= 3.0.0),
        parallel
RoxygenNote: 7.3.3
Collate: 'Data.R' 'GermlineCluster-class.R' 'RcppExports.R' 'piglet.R'
        'allele_cluster.R' 'utils.R' 'allele_genotype.R'
        'community_detection.R' 'piglet-package.R' 'utils-pipe.R'
        'visualization.R'
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2026-02-13 16:44:03 UTC; ayelet
Repository: CRAN
Date/Publication: 2026-02-17 22:30:02 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-08-05 15:11:17 UTC; windows
Archs: x64
