planttfhunter

DOI: 10.18129/B9.bioc.planttfhunter    

This is the development version of planttfhunter; to use it, please install the devel version of Bioconductor.

Identification and classification of plant transcription factors

Bioconductor version: Development (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>

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.2
In Bioconductor since BioC 3.17 (R-4.3)
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_0.99.2.tar.gz
Windows Binary planttfhunter_0.99.2.zip
macOS Binary (x86_64) planttfhunter_0.99.2.tgz
macOS Binary (arm64) planttfhunter_0.99.2.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

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