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planttfhunter

Identification and classification of plant transcription factors


Bioconductor version: Release (3.18)

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. 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). Currently, TFs can be classified in 58 different TF families/subfamilies.

Author: Fabrício Almeida-Silva [aut, cre] , Yves Van de Peer [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>

Citation (from within R, enter citation("planttfhunter")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("planttfhunter")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("planttfhunter")
Genome-wide identification and classification of transcription factors in plant genomes HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, FunctionalGenomics, FunctionalPrediction, GenomeAnnotation, HiddenMarkovModel, Sequencing, Software, Transcription
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends R (>= 4.2.0)
Imports Biostrings, SummarizedExperiment, utils, methods
System Requirements HMMER
URL https://github.com/almeidasilvaf/planttfhunter
Bug Reports https://support.bioconductor.org/t/planttfhunter
See More
Suggests BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package planttfhunter_1.2.0.tar.gz
Windows Binary planttfhunter_1.2.0.zip
macOS Binary (x86_64) planttfhunter_1.2.0.tgz
macOS Binary (arm64) planttfhunter_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/planttfhunter
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/planttfhunter
Bioc Package Browser https://code.bioconductor.org/browse/planttfhunter/
Package Short Url https://bioconductor.org/packages/planttfhunter/
Package Downloads Report Download Stats