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 (3.24)
planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification schemes implemented in PlantTFDB and TAPscan. TFs are also classified into structure-based families, classes, and superclasses as in Plant-TFClass. 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). TFs can be classified in 58 different TF families/subfamilies with PlantTFDB's scheme, and in over 130 families of transcription-associated proteins with TAPscan's scheme.
Author: Fabrício Almeida-Silva [aut, cre]
, Yves Van de Peer [aut]
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("planttfhunter")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.13.1 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 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_1.13.1.tar.gz |
| Windows Binary (x86_64) | planttfhunter_1.13.1.zip |
| macOS Binary (big-sur-x86_64) | planttfhunter_1.13.1.tgz |
| macOS Binary (sonoma-arm64) | planttfhunter_1.13.1.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 |