DESCRIPTION

Package: syntenet
Title: Inference And Analysis Of Synteny Networks
Version: 1.9.1
Date: 2022-03-28
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 = "Tao",
           family = "Zhao",
           role = "aut",
           email = "tao.zhao@nwafu.edu.cn",
           comment = c(ORCID = "0000-0001-7302-6445")),
    person(given = "Kristian K",
           family = "Ullrich",
           role = "aut",
           email = "ullrich@evolbio.mpg.de",
           comment = c(ORCID = "0000-0003-4308-9626")),
    person(given = "Yves",
           family = "Van de Peer",
           role = "aut",
           email = "yves.vandepeer@psb.vib-ugent.be",
           comment = c(ORCID = "0000-0003-4327-3730"))
    )
Description: syntenet can be used to infer synteny networks from 
    whole-genome protein sequences and analyze them. Anchor pairs
    are detected with the MCScanX algorithm, which was ported to this package
    with the Rcpp framework for R and C++ integration. 
    Anchor pairs from synteny analyses are
    treated as an undirected unweighted graph (i.e., a synteny network),
    and users can perform: i. network clustering; ii. phylogenomic profiling 
    (by identifying which species contain which clusters) and; 
    iii. microsynteny-based phylogeny reconstruction with maximum likelihood.
License: GPL-3
URL: https://github.com/almeidasilvaf/syntenet
BugReports: https://support.bioconductor.org/t/syntenet
biocViews: Software,
    NetworkInference,
    FunctionalGenomics,
    ComparativeGenomics,
    Phylogenetics,
    SystemsBiology,
    GraphAndNetwork,
    WholeGenome,
    Network
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Imports:
    Rcpp (>= 1.0.8),
    BiocParallel,
    GenomicRanges,
    rlang,
    Biostrings,
    rtracklayer,
    utils,
    methods,
    igraph,
    stats,
    grDevices,
    RColorBrewer,
    pheatmap,
    ggplot2,
    ggnetwork,
    intergraph
Suggests:
    BiocStyle,
    ggtree,
    labdsv,
    covr,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0),
    xml2,
    networkD3
Config/testthat/edition: 3
VignetteBuilder: knitr
LinkingTo:
    Rcpp,
    testthat
NeedsCompilation: yes
Depends: 
    R (>= 4.2)
LazyData: false