Package: PhyloProfile
Version: 2.4.1
Date: 2026-06-01
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 (>= 4.5.0)
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: cmake libfontconfig1-dev libfreetype6-dev
        libfribidi-dev make libgsl0-dev libharfbuzz-dev libicu-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-06-01 10:02:57 UTC
RemoteUrl: https://github.com/bioc/PhyloProfile
RemoteRef: RELEASE_3_23
RemoteSha: 92deab474c3613e4311396168c4921b857837446
NeedsCompilation: no
Packaged: 2026-06-04 11:19:40 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; ; 2026-06-04 11:21:41 UTC; windows
