Package: PhyloProfile
Version: 2.3.5
Date: 2026-03-11
Title: PhyloProfile
Authors@R: c(
    person("Vinh", "Tran", role = c("aut", "cre"), email = "tran@bio.uni-frankfurt.de", comment=c(ORCID="0000-0001-6772-7595")),
    person("Bastian", "Greshake Tzovaras", role = "aut", email = "bgreshake@googlemail.com"),
    person("Ingo", "Ebersberger", role = "aut", email = "ebersberger@bio.uni-frankfurt.de"),
    person("Carla", "Mölbert", role = "ctb", email = "carla.moelbert@gmx.de"))
Description: PhyloProfile is a tool for exploring complex phylogenetic
        profiles. Phylogenetic profiles, presence/absence patterns of
        genes over a set of species, are commonly used to trace the
        functional and evolutionary history of genes across species and
        time. With PhyloProfile we can enrich regular phylogenetic
        profiles with further data like sequence/structure similarity,
        to make phylogenetic profiling more meaningful. Besides the
        interactive visualisation powered by R-Shiny, the package
        offers a set of further analysis features to gain insights like
        the gene age estimation or core gene identification.
URL: https://github.com/BIONF/PhyloProfile/
BugReports: https://github.com/BIONF/PhyloProfile/issues
License: MIT + file LICENSE
Depends: R (>= 4.4.0)
Encoding: UTF-8
biocViews: Software, Visualization, DataRepresentation,
        MultipleComparison, FunctionalPrediction, DimensionReduction
Imports: ape, bioDist, BiocStyle, Biostrings, bsplus, colourpicker,
        data.table, dplyr, DT, energy, fastcluster, ggplot2, gridExtra,
        htmlwidgets, pbapply, plotly, RColorBrewer, RCurl, Rfast,
        scattermore, shiny, shinycssloaders, shinyFiles, shinyjs,
        stringr, tsne, svglite, umap, xml2, zoo, yaml
RoxygenNote: 7.3.3
Suggests: knitr, rmarkdown, testthat, OmaDB
VignetteBuilder: knitr
Config/pak/sysreqs: libfontconfig1-dev libfreetype6-dev libfribidi-dev
        make libgsl0-dev libharfbuzz-dev libicu-dev libpng-dev
        libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-03-11 10:35:33 UTC
RemoteUrl: https://github.com/bioc/PhyloProfile
RemoteRef: HEAD
RemoteSha: d8059e2479736f587ec6ec1a64f9bbe977b80484
NeedsCompilation: no
Packaged: 2026-03-12 06:57:24 UTC; root
Author: Vinh Tran [aut, cre] (ORCID: <https://orcid.org/0000-0001-6772-7595>),
  Bastian Greshake Tzovaras [aut],
  Ingo Ebersberger [aut],
  Carla Mölbert [ctb]
Maintainer: Vinh Tran <tran@bio.uni-frankfurt.de>
Built: R 4.6.0; ; 2026-03-12 07:00:24 UTC; unix
