Introduction | Installation | Data description | Algorithm description | Identifying and classifying TFs | Counting TFs per family in multiple species at once | Session information | References
Package: planttfhunter 1.13.1
Fabrício Almeida-Silva
planttfhunter: Identification and classification of plant transcription factors
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.
Authors:
planttfhunter_1.13.1.tar.gz
planttfhunter_1.13.1.zip(r-4.7-any)planttfhunter_1.13.1.zip(r-4.6-any)planttfhunter_1.13.1.zip(r-4.5-any)
planttfhunter_1.13.1.tgz(r-4.6-any)planttfhunter_1.13.1.tgz(r-4.5-any)
planttfhunter_1.13.1.tar.gz(r-4.7-any)planttfhunter_1.13.1.tar.gz(r-4.6-any)
planttfhunter_1.13.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
planttfhunter/json (API)
| # Install 'planttfhunter' in R: |
| install.packages('planttfhunter', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/almeidasilvaf/planttfhunter/issues
Datasets:
- gsu - Protein sequences of the algae species Galdieria sulphuraria
- gsu_annotation - Domain annotation for the algae species Galdieria sulphuraria The data set was created using the function 'annotate_domains()'.
- planttfclass_scheme - Correspondence table between TAPscan and Plant-TFClass
- planttfdb_scheme - Data frame of PlantTFDB's TF family classification scheme
- tap_class - Classes of transcription-associated proteins (TAPs) in TAPscan
- tapscan_scheme - Data frame of TAPscan's classification scheme
On BioConductor:planttfhunter-1.13.0(bioc 3.24)planttfhunter-1.12.0(bioc 3.23)
softwaretranscriptionfunctionalpredictiongenomeannotationfunctionalgenomicshiddenmarkovmodelsequencingclassificationfunctional-genomicsgene-familieshidden-markov-modelsplant-genomicsplantsprotein-domainstranscription-factors
Last updated from:e32b42f93a. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 158 | ||
| linux-devel | NOTE | 314 | ||
| source / vignettes | OK | 291 | ||
| linux-release | NOTE | 317 | ||
| macos-release | NOTE | 212 | ||
| macos-oldrel | NOTE | 147 | ||
| windows-devel | NOTE | 140 | ||
| windows-release | NOTE | 174 | ||
| windows-oldrel | NOTE | 172 | ||
| wasm-release | OK | 106 |
Exports:annotate_domainsclassify_tfsget_tf_countshmmer_is_installed
Dependencies:abindBiobaseBiocGenericsBiostringscrayonDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
