Man pages for Bioconductor-mirror/TFBSTools
Software Package for Transcription Factor Binding Site (TFBS) Analysis

calConservation-methodscalConservation method
deleteMatrixHavingID-methodsJASPAR database operations
dmmEM-methodsdmmEM method
getEmissionProbGet the emission distribution parameters.
getMatrixByID-methodsBasic JASPAR database search functionis 'getMatrixByID',...
getMatrixSet-methodsAdvanced JASPAR database search functions 'get_MatrixSet'
getPosProbGet the emission probabilities of nucleotides
IUPAC2MatrixIUPAC2Matrix
MA0004.1Some example PFM matrices.
makeFlatFileDirGenerate "FlatFileDir" directory
MotifSet-classClass '"MotifSet"'
parseMEMEOutputparseMEMEOutput
permuteMatrix-methodspermuteMatrix method
PFMSimilarity-methodsPFMSimilarity method
PWMSimilarity-methodsPWMSimilarity method
readJASPARMatrixRead JASPAR format matrix
readXMLTFFMreadXMLTFFM
rPWMDmm-methodsrPWMDmm method
runMEME-methodsWrapper function for MEME
sampleRangessampleRanges
searchAln-methodssearchAln method
searchPairBSgenome-methodssearchPairBSgenome method
searchSeq-methodssearchSeq method
seqLogoPlot a sequence logo
shannon.entropyCalculate the Shannon entropy
SitePairSet-classClass '"SitePairSet"'
SitePairSetList-classClass '"SitePairSetList"'
SiteSet-classClass '"SiteSet"'
SiteSetList-classClass '"SiteSetList"'
TFBSTools-packageTFBS software package.
TFFM-classThe TFFM class
toGRangesList-methodstoGRangesList function
toICM-methodstoICM method
toPWM-methodstoPWM method
writeGFF3-methods'writeGFF3', 'writeGFF2' functions
XMatrix-class'"XMatrix"' objects
XMatrixList-classClass '"XMatrixList"'
Bioconductor-mirror/TFBSTools documentation built on Aug. 10, 2017, 10:45 a.m.