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"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", 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