planttfhunter
Identification and classification of plant transcription factors
Bioconductor version: 3.23 · Package version: 1.12.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("planttfhunter")Details
| Maintainer | Fabrício Almeida-Silva <fabricio_almeidasilva@hotmail.com> |
| 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>) |
| License | GPL-3 |
| URL | https://github.com/almeidasilvaf/planttfhunter |
| Bug Reports | https://support.bioconductor.org/t/planttfhunter |
| System Requirements | HMMER <http://hmmer.org/> |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, FunctionalGenomics, FunctionalPrediction, GenomeAnnotation, HiddenMarkovModel, Sequencing, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/planttfhunter/ |
Citation
From within R, enter citation("planttfhunter"):
Fabrício Almeida-Silva, Yves Van de Peer. planttfhunter: Identification and classification of plant transcription factors. doi:10.18129/B9.bioc.planttfhunter, R package version 1.12.0, https://bioconductor.org/packages/planttfhunter.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | planttfhunter_1.12.0.tar.gz |
| Windows binary (x86_64) | planttfhunter_1.12.0.zip |
| macOS binary (arm64) | planttfhunter_1.12.0.tgz |
| macOS binary (x86_64) | planttfhunter_1.12.0.tgz |
Dependencies
Depends: R (>= 4.2.0)
Imports: Biostrings, SummarizedExperiment, utils, methods
Suggests: BiocStyle, covr, sessioninfo, knitr, rmarkdown, testthat (>= 3.0.0)