Package: planttfhunter 1.7.0

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:Fabrício Almeida-Silva [aut, cre], Yves Van de Peer [aut]

planttfhunter_1.7.0.tar.gz
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planttfhunter.pdf |planttfhunter.html✨
planttfhunter/json (API)
NEWS

# 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-1.7.0(bioc 3.21)planttfhunter-1.6.0(bioc 3.20)

softwaretranscriptionfunctionalpredictiongenomeannotationfunctionalgenomicshiddenmarkovmodelsequencingclassificationfunctional-genomicsgene-familieshidden-markov-modelsplant-genomicsplantsprotein-domainstranscription-factors

4.00 score 5 scripts 180 downloads 4 exports 29 dependencies

Last updated 4 months agofrom:b3714d58f6. Checks:7 OK, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 16 2025
R-4.5-winOKFeb 16 2025
R-4.5-macWARNINGFeb 16 2025
R-4.5-linuxOKFeb 16 2025
R-4.4-winOKFeb 16 2025
R-4.4-macOKFeb 16 2025
R-4.3-winOKFeb 16 2025
R-4.3-macOKFeb 16 2025

Exports:annotate_pfamclassify_tfsget_tf_countshmmer_is_installed

Dependencies:abindaskpassBiobaseBiocGenericsBiostringscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVector

Genome-wide identification and classification of transcription factors in plant genomes

Fabricio Almeida-Silva, Yves Van de Peer

Rendered fromvignette_planttfhunter.Rmdusingknitr::rmarkdownon Feb 16 2025.

Last update: 2022-11-14
Started: 2022-10-11