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
Config/pak/sysreqs: zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-10-06 08:23:03 UTC
RemoteUrl: https://github.com/bioc/planttfhunter
RemoteRef: HEAD
RemoteSha: e32b42f93a007723467da1a361c894c5e24c4b52
NeedsCompilation: no
Packaged: 2026-10-07 08:39:10 UTC; root
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>