IUPAC2Matrix            IUPAC2Matrix
MA0004.1                Some example PFM matrices.
MotifSet                Class '"MotifSet"'
PFMSimilarity-methods   PFMSimilarity method
PWMSimilarity-methods   PWMSimilarity method
SitePairSet             Class '"SitePairSet"'
SitePairSetList-class   Class '"SitePairSetList"'
SiteSet                 Class '"SiteSet"'
SiteSetList             Class '"SiteSetList"'
TFBSTools               TFBS software package.
TFFM                    The TFFM class
XMatrix                 '"XMatrix"' objects
XMatrixList             Class '"XMatrixList"'
calConservation-methods
                        calConservation method
deleteMatrixHavingID    JASPAR database operations
dmmEM-methods           dmmEM method
getEmissionProb         Get the emission distribution parameters.
getMatrixByID           Basic JASPAR database search functionis
                        'getMatrixByID', 'getMatrixByName'
getMatrixSet            Advanced JASPAR database search functions
                        'get_MatrixSet'
getPosProb              Get the emission probabilities of nucleotides
makeFlatFileDir         Generate "FlatFileDir" directory
parseMEMEOutput         parseMEMEOutput
permuteMatrix-methods   permuteMatrix method
rPWMDmm-methods         rPWMDmm method
readJASPARMatrix        Read JASPAR format matrix
readXMLTFFM             readXMLTFFM
runMEME                 Wrapper function for MEME
sampleRanges            sampleRanges
searchAln               searchAln method
searchPairBSgenome-methods
                        searchPairBSgenome method
searchSeq               searchSeq method
seqLogo                 Plot a sequence logo
shannon.entropy         Calculate the Shannon entropy
toGRangesList-methods   toGRangesList function
toICM                   toICM method
toPWM                   toPWM method
writeGFF3-methods       'writeGFF3', 'writeGFF2' functions
