Package: planttfhunter
Title: Identification and classification of plant transcription factors
Version: 1.13.1
Date: 2022-03-10
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: planttfhunter is used to identify plant transcription factors (TFs) 
    from protein sequence data and classify them into families and subfamilies
    using the classification schemes implemented in PlantTFDB and TAPscan.
    TFs are also classified into structure-based families, classes, and
    superclasses as in Plant-TFClass.
    TFs are identified using pre-built hidden Markov model profiles
    for DNA-binding domains. Then, auxiliary and forbidden domains are
    used with DNA-binding domains to classify TFs into families and
    subfamilies (when applicable). TFs can be classified in
    58 different TF families/subfamilies with PlantTFDB's scheme, and in
    over 130 families of transcription-associated proteins with
    TAPscan's scheme.
License: GPL-3
URL: https://github.com/almeidasilvaf/planttfhunter
BugReports: https://support.bioconductor.org/t/planttfhunter
biocViews: Software, Transcription, FunctionalPrediction,
        GenomeAnnotation, FunctionalGenomics, HiddenMarkovModel,
        Sequencing, Classification
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.1
SystemRequirements: HMMER <http://hmmer.org/>
Imports: Biostrings, SummarizedExperiment, utils, methods
Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>=
        3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
Depends: R (>= 4.2.0)
LazyData: false
git_url: https://git.bioconductor.org/packages/planttfhunter
git_branch: devel
git_last_commit: e32b42f
git_last_commit_date: 2026-10-06
Repository: Bioconductor 3.24
Date/Publication: 2026-10-06
NeedsCompilation: no
Packaged: 2026-10-06 22:23:22 UTC; biocbuild
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 4.6.1; ; 2026-10-07 06:20:42 UTC; unix
