{
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  "Package": "TFBSTools",
  "Version": "1.51.0",
  "Date": "2025-07-22",
  "Title": "Software Package for Transcription Factor Binding Site (TFBS)\nAnalysis",
  "Description": "TFBSTools is a package for the analysis and manipulation\nof transcription factor binding sites. It includes matrices\nconversion between Position Frequency Matirx (PFM), Position\nWeight Matirx (PWM) and Information Content Matrix (ICM). It\ncan also scan putative TFBS from sequence/alignment, query\nJASPAR database and provides a wrapper of de novo motif\ndiscovery software.",
  "Authors@R": "person(\"Ge\", \"Tan\", email=\"ge_tan@live.com\",\nrole = c(\"aut\", \"cre\"))",
  "VignetteBuilder": "knitr",
  "License": "GPL-2",
  "URL": "https://github.com/ge11232002/TFBSTools",
  "BugReports": "https://github.com/ge11232002/TFBSTools/issues",
  "Type": "Package",
  "biocViews": "MotifAnnotation, GeneRegulation, MotifDiscovery,\nTranscription, Alignment",
  "NeedsCompilation": "yes",
  "LazyData": "yes",
  "Collate": "AllGenerics.r AllClasses.r show-methods.r util-methods.r\nXMatrix-methods.r XMatrixList-methods.r SiteSet-methods.r\ncoercion-methods.r DB-methods.r JASPAR.R\nPairwiseAlignment-methods.r ICM-methods.r PWM-methods.r\nMotif-methods.r PFM-methods.r Wrappers-methods.r\nDirichletMixture.r TFFM.R TFFMseqLogo.R IO.R Enrichment.R",
  "Config/pak/sysreqs": "make libgsl0-dev libbz2-dev liblzma-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:38:20 UTC",
  "RemoteUrl": "https://github.com/bioc/TFBSTools",
  "RemoteRef": "HEAD",
  "RemoteSha": "f7b3785310fe63785abc69c5e84f6f095979725d",
  "Packaged": {
    "Date": "2026-05-30 09:45:47 UTC",
    "User": "root"
  },
  "Author": "Ge Tan [aut, cre]",
  "Maintainer": "Ge Tan <ge_tan@live.com>",
  "MD5sum": "84fad87a4bd0d546a563c2f269ef9b5c",
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  "_exports": [
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    "as.matrix",
    "bg",
    "calConservation",
    "colSums",
    "consensusMatrix",
    "deleteMatrixHavingID",
    "dmmEM",
    "end",
    "getEmissionProb",
    "getMatrixByID",
    "getMatrixByName",
    "getMatrixSet",
    "getPosProb",
    "ICMatrix",
    "ICMatrixList",
    "ID",
    "initializeJASPARDB",
    "IUPAC2Matrix",
    "makeFlatFileDir",
    "Matrix",
    "Matrix<-",
    "matrixClass",
    "matrixType",
    "MotifSet",
    "name",
    "ncol",
    "parseMEMEOutput",
    "permuteMatrix",
    "PFMatrix",
    "PFMatrixList",
    "PFMSimilarity",
    "pvalues",
    "PWMatrix",
    "PWMatrixList",
    "PWMSimilarity",
    "readJASPARMatrix",
    "readXMLTFFM",
    "relScore",
    "reverseComplement",
    "rowSums",
    "rPWMDmm",
    "runMEME",
    "sampleRanges",
    "searchAln",
    "searchPairBSgenome",
    "searchSeq",
    "seqLogo",
    "shannon.entropy",
    "showAsCell",
    "SitePairSet",
    "SitePairSetList",
    "SiteSet",
    "SiteSetList",
    "sitesSeq",
    "start",
    "storeMatrix",
    "tags",
    "TFFMDetail",
    "TFFMFirst",
    "toICM",
    "toPWM",
    "totalIC",
    "views",
    "writeGFF2",
    "writeGFF3",
    "XMatrixList"
  ],
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    {
      "name": "MA0003.2",
      "title": "Some example PFM matrices.",
      "object": "MA0003.2",
      "class": [
        "PFMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "MA0004.1",
      "title": "Some example PFM matrices.",
      "object": "MA0004.1",
      "class": [
        "PFMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "MA0043",
      "title": "Some example PFM matrices.",
      "object": "MA0043",
      "class": [
        "PFMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "MA0048",
      "title": "Some example PFM matrices.",
      "object": "MA0048",
      "class": [
        "PFMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "TFBSTools-package",
      "title": "TFBS software package.",
      "topics": [
        "TFBSTools"
      ]
    },
    {
      "page": "calConservation-methods",
      "title": "calConservation method",
      "topics": [
        "calConservation",
        "calConservation,character,character-method",
        "calConservation,character,missing-method",
        "calConservation,DNAString,DNAString-method",
        "calConservation,DNAStringSet,missing-method",
        "calConservation-methods"
      ]
    },
    {
      "page": "deleteMatrixHavingID-methods",
      "title": "JASPAR database operations",
      "topics": [
        "deleteMatrixHavingID",
        "deleteMatrixHavingID,character-method",
        "deleteMatrixHavingID,JASPAR2014-method",
        "deleteMatrixHavingID,JASPAR2016-method",
        "deleteMatrixHavingID,JASPAR2018-method",
        "deleteMatrixHavingID,JASPAR2020-method",
        "deleteMatrixHavingID,JASPAR2022-method",
        "deleteMatrixHavingID,SQLiteConnection-method",
        "initializeJASPARDB",
        "initializeJASPARDB,character-method",
        "initializeJASPARDB,JASPAR2014-method",
        "initializeJASPARDB,JASPAR2016-method",
        "initializeJASPARDB,JASPAR2018-method",
        "initializeJASPARDB,JASPAR2020-method",
        "initializeJASPARDB,JASPAR2022-method",
        "initializeJASPARDB,SQLiteConnection-method",
        "storeMatrix",
        "storeMatrix,character,PFMatrix-method",
        "storeMatrix,character,PFMatrixList-method",
        "storeMatrix,JASPAR2014,PFMatrix-method",
        "storeMatrix,JASPAR2014,PFMatrixList-method",
        "storeMatrix,JASPAR2016,PFMatrix-method",
        "storeMatrix,JASPAR2016,PFMatrixList-method",
        "storeMatrix,JASPAR2018,PFMatrix-method",
        "storeMatrix,JASPAR2018,PFMatrixList-method",
        "storeMatrix,JASPAR2020,PFMatrix-method",
        "storeMatrix,JASPAR2020,PFMatrixList-method",
        "storeMatrix,JASPAR2022,PFMatrix-method",
        "storeMatrix,JASPAR2022,PFMatrixList-method",
        "storeMatrix,SQLiteConnection,PFMatrix-method",
        "storeMatrix,SQLiteConnection,PFMatrixList-method",
        "storeMatrix-methods"
      ]
    },
    {
      "page": "dmmEM-methods",
      "title": "dmmEM method",
      "topics": [
        "dmmEM",
        "dmmEM,ANY-method",
        "dmmEM,matrix-method",
        "dmmEM,PFMatrixList-method",
        "dmmEM-methods"
      ]
    },
    {
      "page": "getEmissionProb",
      "title": "Get the emission distribution parameters.",
      "topics": [
        "getEmissionProb",
        "getEmissionProb,TFFMDetail-method",
        "getEmissionProb,TFFMFirst-method"
      ]
    },
    {
      "page": "getMatrixByID-methods",
      "title": "Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'",
      "topics": [
        "getMatrixByID",
        "getMatrixByID,character-method",
        "getMatrixByID,JASPAR2014-method",
        "getMatrixByID,JASPAR2016-method",
        "getMatrixByID,JASPAR2018-method",
        "getMatrixByID,JASPAR2020-method",
        "getMatrixByID,JASPAR2022-method",
        "getMatrixByID,SQLiteConnection-method",
        "getMatrixByName",
        "getMatrixByName,character-method",
        "getMatrixByName,JASPAR2014-method",
        "getMatrixByName,JASPAR2016-method",
        "getMatrixByName,JASPAR2018-method",
        "getMatrixByName,JASPAR2020-method",
        "getMatrixByName,JASPAR2022-method",
        "getMatrixByName,SQLiteConnection-method"
      ]
    },
    {
      "page": "getMatrixSet-methods",
      "title": "Advanced JASPAR database search functions 'get_MatrixSet'",
      "topics": [
        "getMatrixSet",
        "getMatrixSet,character-method",
        "getMatrixSet,JASPAR2014-method",
        "getMatrixSet,JASPAR2016-method",
        "getMatrixSet,JASPAR2018-method",
        "getMatrixSet,JASPAR2020-method",
        "getMatrixSet,JASPAR2022-method",
        "getMatrixSet,SQLiteConnection-method"
      ]
    },
    {
      "page": "getPosProb",
      "title": "Get the emission probabilities of nucleotides",
      "topics": [
        "getPosProb",
        "getPosProb,TFFMDetail-method",
        "getPosProb,TFFMFirst-method"
      ]
    },
    {
      "page": "IUPAC2Matrix",
      "title": "IUPAC2Matrix",
      "topics": [
        "IUPAC2Matrix"
      ]
    },
    {
      "page": "MA0004.1",
      "title": "Some example PFM matrices.",
      "topics": [
        "MA0003.2",
        "MA0004.1",
        "MA0043",
        "MA0048"
      ]
    },
    {
      "page": "makeFlatFileDir",
      "title": "Generate \"FlatFileDir\" directory",
      "topics": [
        "makeFlatFileDir"
      ]
    },
    {
      "page": "MotifSet-class",
      "title": "Class '\"MotifSet\"'",
      "topics": [
        "consensusMatrix,MotifSet-method",
        "length,MotifSet-method",
        "MotifSet",
        "MotifSet-class",
        "sitesSeq",
        "sitesSeq,MotifSet-method",
        "[,MotifSet,ANY,ANY,ANY-method",
        "[,MotifSet,ANY,ANY-method",
        "[,MotifSet-method"
      ]
    },
    {
      "page": "parseMEMEOutput",
      "title": "parseMEMEOutput",
      "topics": [
        "parseMEMEOutput"
      ]
    },
    {
      "page": "permuteMatrix-methods",
      "title": "permuteMatrix method",
      "topics": [
        "permuteMatrix",
        "permuteMatrix,matrix-method",
        "permuteMatrix,PFMatrix-method",
        "permuteMatrix,PFMatrixList-method",
        "permuteMatrix-methods"
      ]
    },
    {
      "page": "PFMSimilarity-methods",
      "title": "PFMSimilarity method",
      "topics": [
        "PFMSimilarity",
        "PFMSimilarity,matrix,character-method",
        "PFMSimilarity,matrix,matrix-method",
        "PFMSimilarity,matrix,PFMatrix-method",
        "PFMSimilarity,PFMatrix,character-method",
        "PFMSimilarity,PFMatrix,matrix-method",
        "PFMSimilarity,PFMatrix,PFMatrix-method",
        "PFMSimilarity,PFMatrixList,character-method",
        "PFMSimilarity,PFMatrixList,matrix-method",
        "PFMSimilarity,PFMatrixList,PFMatrix-method",
        "PFMSimilarity-methods"
      ]
    },
    {
      "page": "PWMSimilarity-methods",
      "title": "PWMSimilarity method",
      "topics": [
        "PWMSimilarity",
        "PWMSimilarity,matrix,matrix-method",
        "PWMSimilarity,matrix,PWMatrix-method",
        "PWMSimilarity,PWMatrix,matrix-method",
        "PWMSimilarity,PWMatrix,PWMatrix-method",
        "PWMSimilarity,PWMatrixList,matrix-method",
        "PWMSimilarity,PWMatrixList,PWMatrix-method",
        "PWMSimilarity,PWMatrixList,PWMatrixList-method",
        "PWMSimilarity-methods"
      ]
    },
    {
      "page": "readJASPARMatrix",
      "title": "Read JASPAR format matrix",
      "topics": [
        "readJASPARMatrix"
      ]
    },
    {
      "page": "readXMLTFFM",
      "title": "readXMLTFFM",
      "topics": [
        "readXMLTFFM"
      ]
    },
    {
      "page": "rPWMDmm-methods",
      "title": "rPWMDmm method",
      "topics": [
        "rPWMDmm",
        "rPWMDmm,matrix-method",
        "rPWMDmm,PFMatrix-method",
        "rPWMDmm,PFMatrixList-method",
        "rPWMDmm-methods"
      ]
    },
    {
      "page": "runMEME-methods",
      "title": "Wrapper function for MEME",
      "topics": [
        "runMEME",
        "runMEME,character-method",
        "runMEME,DNAStringSet-method"
      ]
    },
    {
      "page": "sampleRanges",
      "title": "sampleRanges",
      "topics": [
        "sampleRanges"
      ]
    },
    {
      "page": "searchAln-methods",
      "title": "searchAln method",
      "topics": [
        "searchAln",
        "searchAln,PWMatrix,Axt,missing-method",
        "searchAln,PWMatrix,character,character-method",
        "searchAln,PWMatrix,character,missing-method",
        "searchAln,PWMatrix,DNAString,DNAString-method",
        "searchAln,PWMatrix,DNAStringSet,missing-method",
        "searchAln,PWMatrixList,character,character-method",
        "searchAln,PWMatrixList,character,missing-method",
        "searchAln,PWMatrixList,DNAString,DNAString-method",
        "searchAln,PWMatrixList,DNAStringSet,missing-method"
      ]
    },
    {
      "page": "searchPairBSgenome-methods",
      "title": "searchPairBSgenome method",
      "topics": [
        "searchPairBSgenome",
        "searchPairBSgenome,PWMatrix-method",
        "searchPairBSgenome,PWMatrixList-method",
        "searchPairBSgenome-methods"
      ]
    },
    {
      "page": "searchSeq-methods",
      "title": "searchSeq method",
      "topics": [
        "searchSeq",
        "searchSeq,PWMatrix-method",
        "searchSeq,PWMatrixList-method",
        "searchSeq-methods"
      ]
    },
    {
      "page": "seqLogo",
      "title": "Plot a sequence logo",
      "topics": [
        "seqLogo",
        "seqLogo,ICMatrix-method",
        "seqLogo,TFFM-method"
      ]
    },
    {
      "page": "shannon.entropy",
      "title": "Calculate the Shannon entropy",
      "topics": [
        "shannon.entropy"
      ]
    },
    {
      "page": "SitePairSet-class",
      "title": "Class '\"SitePairSet\"'",
      "topics": [
        "as.data.frame,SitePairSet-method",
        "length,SitePairSet-method",
        "site1,SitePairSet-method",
        "site2,SitePairSet-method",
        "SitePairSet",
        "SitePairSet-class"
      ]
    },
    {
      "page": "SitePairSetList-class",
      "title": "Class '\"SitePairSetList\"'",
      "topics": [
        "as.data.frame,SitePairSetList-method",
        "SitePairSetList",
        "SitePairSetList-class"
      ]
    },
    {
      "page": "SiteSet-class",
      "title": "Class '\"SiteSet\"'",
      "topics": [
        "as.data.frame,SiteSet-method",
        "c,SiteSet-method",
        "c-methods",
        "end,SiteSet-method",
        "length,SiteSet-method",
        "pattern,SiteSet-method",
        "primary,SiteSet-method",
        "pvalues",
        "pvalues,SiteSet-method",
        "relScore",
        "relScore,SiteSet-method",
        "score,SiteSet-method",
        "seqname,SiteSet-method",
        "show,SiteSet-method",
        "SiteSet",
        "SiteSet-class",
        "sitesource,SiteSet-method",
        "start,SiteSet-method",
        "strand,SiteSet-method",
        "views",
        "views,SiteSet-method",
        "[,SiteSet,ANY,ANY,ANY-method",
        "[,SiteSet,ANY,ANY-method",
        "[,SiteSet-method"
      ]
    },
    {
      "page": "SiteSetList-class",
      "title": "Class '\"SiteSetList\"'",
      "topics": [
        "as.data.frame,SiteSetList-method",
        "pvalues,SiteSetList-method",
        "relScore,SiteSetList-method",
        "SiteSetList",
        "SiteSetList-class"
      ]
    },
    {
      "page": "TFFM-class",
      "title": "The TFFM class",
      "topics": [
        "ncol,TFFMDetail-method",
        "ncol,TFFMFirst-method",
        "TFFM",
        "TFFMDetail",
        "TFFMFirst",
        "totalIC,TFFM-method"
      ]
    },
    {
      "page": "toGRangesList-methods",
      "title": "toGRangesList function",
      "topics": [
        "toGRangesList",
        "toGRangesList,SitePairSetList,Axt-method",
        "toGRangesList-methods"
      ]
    },
    {
      "page": "toICM-methods",
      "title": "toICM method",
      "topics": [
        "toICM",
        "toICM,character-method",
        "toICM,DNAStringSet-method",
        "toICM,matrix-method",
        "toICM,PFMatrix-method",
        "toICM,PFMatrixList-method"
      ]
    },
    {
      "page": "toPWM-methods",
      "title": "toPWM method",
      "topics": [
        "toPWM",
        "toPWM,character-method",
        "toPWM,DNAStringSet-method",
        "toPWM,matrix-method",
        "toPWM,PFMatrix-method",
        "toPWM,PFMatrixList-method"
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    },
    {
      "page": "writeGFF3-methods",
      "title": "'writeGFF3', 'writeGFF2' functions",
      "topics": [
        "writeGFF2",
        "writeGFF2,SitePairSet-method",
        "writeGFF2,SitePairSetList-method",
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        "writeGFF3",
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        "writeGFF3,SiteSetList-method",
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    },
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      "page": "XMatrix-class",
      "title": "'\"XMatrix\"' objects",
      "topics": [
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        "bg",
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        "bg<-,XMatrix-method",
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        "XMatrix",
        "XMatrix-class",
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      ]
    },
    {
      "page": "XMatrixList-class",
      "title": "Class '\"XMatrixList\"'",
      "topics": [
        "bg,XMatrixList-method",
        "ICMatrixList",
        "ICMatrixList-class",
        "ID,XMatrixList-method",
        "Matrix,XMatrixList-method",
        "matrixClass,XMatrixList-method",
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        "PFMatrixList",
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        "PWMatrixList",
        "PWMatrixList-class",
        "showAsCell,XMatrixList-method",
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  ],
  "_vignettes": [
    {
      "source": "TFBSTools.Rmd",
      "filename": "TFBSTools.html",
      "title": "Transcription factor binding site (TFBS) analysis with the \"TFBSTools\" package",
      "author": "Ge Tan",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "S4 classes in TFBSTools",
        "XMatrix and its subclasses",
        "XMatrixList and its subclasses",
        "SiteSet, SiteSetList, SitePairSet and SitePairSetList",
        "MotifSet",
        "TFFM and its subclasses",
        "Database interfaces for JASPAR2014 database",
        "Search JASPAR2014 database",
        "Store, delete and initialize JASPAR2014 database",
        "PFM, PWM and ICM methods",
        "PFM to PWM",
        "PFM to ICM",
        "Align PFM to a custom matrix or IUPAC string",
        "PWM similarity",
        "Dynamic random profile generation",
        "TFFM methods",
        "The graphical representation of TFFM",
        "Scan sequence and alignments with PWM pattern",
        "searchSeq",
        "searchAln",
        "searchPairBSgenome",
        "Use de novo motif discovery software",
        "MEME",
        "Session info",
        "References"
      ],
      "created": "2015-11-17 13:18:55",
      "modified": "2025-03-12 16:25:58",
      "commits": 8
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