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'))

Peer review:

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 146 downloads 4 exports 30 dependencies

Last updated 25 days agofrom:b3714d58f6. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 18 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

Exports:annotate_pfamclassify_tfsget_tf_countshmmer_is_installed

Dependencies:abindaskpassBiobaseBiocGenericsBiostringscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVectorzlibbioc

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

Fabricio Almeida-Silva, Yves Van de Peer

Rendered fromvignette_planttfhunter.Rmdusingknitr::rmarkdownon Nov 18 2024.

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