Package: doubletrouble
Title: Identification and classification of duplicated genes
Version: 1.11.0
Date: 2024-03-19
Authors@R: 
    c(
    person(given = "Fabrício",
           family = "Almeida-Silva",
           role = c("aut", "cre"),
           email = "fabricio_almeidasilva@hotmail.com",
           comment = c(ORCID = "0000-0002-5314-2964")),
    person(given = "Yves",
           family = "Van de Peer",
           role = "aut",
           email = "yves.vandepeer@psb.vib-ugent.be",
           comment = c(ORCID = "0000-0003-4327-3730"))
    )
Description: doubletrouble aims to identify duplicated genes from
        whole-genome protein sequences and classify them based on their
        modes of duplication. The duplication modes are i. segmental
        duplication (SD); ii. tandem duplication (TD); iii. proximal
        duplication (PD); iv. transposed duplication (TRD) and; v.
        dispersed duplication (DD). Transposon-derived duplicates (TRD)
        can be further subdivided into rTRD (retrotransposon-derived
        duplication) and dTRD (DNA transposon-derived duplication). If
        users want a simpler classification scheme, duplicates can also
        be classified into SD- and SSD-derived (small-scale
        duplication) gene pairs. Besides classifying gene pairs, users
        can also classify genes, so that each gene is assigned a unique
        mode of duplication. Users can also calculate substitution
        rates per substitution site (i.e., Ka and Ks) from duplicate
        pairs, find peaks in Ks distributions with Gaussian Mixture
        Models (GMMs), and classify gene pairs into age groups based on
        Ks peaks.
License: GPL-3
URL: https://github.com/almeidasilvaf/doubletrouble
BugReports: https://support.bioconductor.org/t/doubletrouble
biocViews: Software, WholeGenome, ComparativeGenomics,
        FunctionalGenomics, Phylogenetics, Network, Classification
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports: syntenet, GenomicRanges, Biostrings, mclust, MSA2dist (>=
        1.1.5), ggplot2, rlang, stats, utils, AnnotationDbi,
        GenomicFeatures
Depends: R (>= 4.2.0)
Suggests: txdbmaker, testthat (>= 3.0.0), knitr, feature, patchwork,
        BiocStyle, rmarkdown, covr, sessioninfo
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: libglpk-dev make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:20:05 UTC
RemoteUrl: https://github.com/bioc/doubletrouble
RemoteRef: HEAD
RemoteSha: 60c6759a4c70a4fcb05dfd62a9206172a1c2f883
NeedsCompilation: no
Packaged: 2026-02-21 06:48:17 UTC; root
Author: Fabrício Almeida-Silva [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5314-2964>),
  Yves Van de Peer [aut] (ORCID: <https://orcid.org/0000-0003-4327-3730>)
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com>
Built: R 4.6.0; ; 2026-02-21 06:50:39 UTC; unix
