DESCRIPTION

Package: doubletrouble
Title: Identification and classification of duplicated genes
Version: 1.5.4
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