Introduction | Installation | Data description | Algorithm description | Identifying and classifying TFs | Counting TFs per family in multiple species at once | Session information | References
Package: planttfhunter 1.13.0
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 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.
Authors:
planttfhunter_1.13.0.tar.gz
planttfhunter_1.13.0.zip(r-4.7)planttfhunter_1.13.0.zip(r-4.6)planttfhunter_1.13.0.zip(r-4.5)
planttfhunter_1.13.0.tgz(r-4.6-any)planttfhunter_1.13.0.tgz(r-4.5-any)
planttfhunter_1.13.0.tar.gz(r-4.7-any)planttfhunter_1.13.0.tar.gz(r-4.6-any)
planttfhunter_1.13.0.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:
- classification_scheme - Data frame of TF family classification scheme
- 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 funcion 'annotate_pfam()' in local mode.
- gsu_families - TFs families of the algae species Galdieria sulphuraria The data set was created using the funcion 'classify_tfs()'.
- tf_counts - TF counts per family in 4 simulated species
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:a96490f571. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 165 | ||
| linux-devel-x86_64 | OK | 277 | ||
| source / vignettes | OK | 249 | ||
| linux-release-x86_64 | OK | 270 | ||
| macos-release-arm64 | OK | 147 | ||
| macos-oldrel-arm64 | OK | 196 | ||
| windows-devel | OK | 207 | ||
| windows-release | OK | 200 | ||
| windows-oldrel | OK | 178 | ||
| wasm-release | OK | 123 |
Exports:annotate_pfamclassify_tfsget_tf_countshmmer_is_installed
Dependencies:abindBiobaseBiocGenericsBiostringscrayonDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
