Package: piglet
Title: Program for Inferring Immunoglobulin Allele Similarity Clusters
        and Genotypes
Version: 1.3.0
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
URL: https://github.com/ayeletperes/piglet
BugReports: https://github.com/ayeletperes/piglet/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
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), RColorBrewer
        (>= 1.1.2), ggplot2 (>= 3.3.6), circlize (>= 0.4.15), gridExtra
        (>= 2.3), 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, bookdown, dplyr, ggtree
        (>= 3.0.0), testthat (>= 3.0.0)
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
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libxml2-dev libx11-dev xz-utils zlib1g-dev
Repository: https://ayeletperes.r-universe.dev
Date/Publication: 2026-06-20 17:46:51 UTC
RemoteUrl: https://github.com/ayeletperes/piglet
RemoteRef: HEAD
RemoteSha: 45063019e3add0bcbee66076ad317e924ccb6493
NeedsCompilation: yes
Packaged: 2026-06-20 19:21:45 UTC; root