planttfhunter

DOI: 10.18129/B9.bioc.planttfhunter  

Identification and classification of plant transcription factors

Bioconductor version: Release (3.17)

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>

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")

 

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

Details

biocViews	Classification, FunctionalGenomics, FunctionalPrediction, GenomeAnnotation, HiddenMarkovModel, Sequencing, Software, Transcription
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.2.0)
Imports	Biostrings, SummarizedExperiment, utils, methods
LinkingTo
Suggests	BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0)
SystemRequirements	HMMER
Enhances
URL	https://github.com/almeidasilvaf/planttfhunter
BugReports	https://support.bioconductor.org/t/planttfhunter
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	planttfhunter_1.0.0.tar.gz
Windows Binary	planttfhunter_1.0.0.zip
macOS Binary (x86_64)	planttfhunter_1.0.0.tgz
macOS Binary (arm64)	planttfhunter_1.0.0.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
Old Source Packages for BioC 3.17	Source Archive