{
"_id": "6a493ef4a19c9318096e7e1b",
"Package": "planttfhunter",
"Title": "Identification and classification of plant transcription factors",
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"Date": "2022-03-10",
"Authors@R": "c(\nperson(given = \"Fabrício\",\nfamily = \"Almeida-Silva\",\nrole = c(\"aut\", \"cre\"),\nemail = \"fabricio_almeidasilva@hotmail.com\",\ncomment = c(ORCID = \"0000-0002-5314-2964\")),\nperson(given = \"Yves\",\nfamily = \"Van de Peer\",\nrole = \"aut\",\nemail = \"yves.vandepeer@psb.vib-ugent.be\",\ncomment = c(ORCID = \"0000-0003-4327-3730\"))\n)",
"Description": "planttfhunter is used to identify plant transcription\nfactors (TFs) from protein sequence data and classify them into\nfamilies and subfamilies using the classification scheme\nimplemented in PlantTFDB. TFs are identified using pre-built\nhidden Markov model profiles for DNA-binding domains. Then,\nauxiliary and forbidden domains are used with DNA-binding\ndomains to classify TFs into families and subfamilies (when\napplicable). Currently, TFs can be classified in 58 different\nTF families/subfamilies.",
"License": "GPL-3",
"URL": "https://github.com/almeidasilvaf/planttfhunter",
"BugReports": "https://support.bioconductor.org/t/planttfhunter",
"biocViews": "Software, Transcription, FunctionalPrediction,\nGenomeAnnotation, FunctionalGenomics, HiddenMarkovModel,\nSequencing, Classification",
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"VignetteBuilder": "knitr",
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"Repository": "https://bioc.r-universe.dev",
"Date/Publication": "2026-04-28 12:59:30 UTC",
"RemoteUrl": "https://github.com/bioc/planttfhunter",
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"User": "root"
},
"Author": "Fabrício Almeida-Silva [aut, cre] (ORCID:\n),\nYves Van de Peer [aut] (ORCID: )",
"Maintainer": "Fabrício Almeida-Silva ",
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"note": 3
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},
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"name": "Fabrício Almeida-Silva",
"email": "fabricio_almeidasilva@hotmail.com",
"login": "almeidasilvaf",
"bluesky": "@almeidasilvaf.bsky.social",
"description": "Bioinformatics. Network biology. Plant genomics and evolution. #rstats addict.",
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"genomeannotation",
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"hiddenmarkovmodel",
"sequencing",
"classification",
"functional-genomics",
"gene-families",
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"_homeurl": "https://github.com/almeidasilvaf/planttfhunter",
"_realowner": "bioc",
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"_exports": [
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"classify_tfs",
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],
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"title": "Data frame of TF family classification scheme",
"object": "classification_scheme",
"file": "classification_scheme.rda",
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"DBD",
"Auxiliary",
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"object": "gsu",
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},
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"title": "Domain annotation for the algae species Galdieria sulphuraria The data set was created using the funcion 'annotate_pfam()' in local mode.",
"object": "gsu_annotation",
"file": "gsu_annotation.rda",
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],
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},
{
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"title": "TFs families of the algae species Galdieria sulphuraria The data set was created using the funcion 'classify_tfs()'.",
"object": "gsu_families",
"file": "gsu_families.rda",
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"fields": [
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},
{
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"_help": [
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"page": "annotate_pfam",
"title": "Annotate proteins sequences with PFAM domains",
"topics": [
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"title": "Data frame of TF family classification scheme",
"topics": [
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},
{
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"title": "Identify TFs and classify them in families",
"topics": [
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},
{
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"topics": [
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},
{
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},
{
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"title": "Check if HMMER is installed",
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