planttfhunter
This is the development version of planttfhunter; for the stable release version, see planttfhunter.
Identification and classification of plant transcription factors
Bioconductor version: Development (3.21)
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: FabrÃcio Almeida-Silva [aut, cre] (ORCID:
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("planttfhunter")):
Installation
To install this package, start R (version "4.5") 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")| Genome-wide identification and classification of transcription factors in plant genomes | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, FunctionalGenomics, FunctionalPrediction, GenomeAnnotation, HiddenMarkovModel, Sequencing, Software, Transcription |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | planttfhunter_1.7.0.tar.gz |
| Windows Binary (x86_64) | planttfhunter_1.7.0.zip |
| macOS Binary (x86_64) | planttfhunter_1.7.0.tgz |
| macOS Binary (arm64) | planttfhunter_1.7.0.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 |