addAnchorMatrix | Add some prefixed sequence to existing energy matrix |
as.Coefficients | Convert energy matrix to energy model coefficients Encoding... |
as.PEM | Convert defined subject to position energy matrix |
buildEnergyModel | Build energy model based on Sequence-Energy relationship |
buildMethylationModel | Build model of methylation effect based on pair-wise compared... |
composeMotif | Build composite motif based on two existing motifs with... |
countMismatch | Count the number of mismatches of sequence(s) to some... |
decomposeMotif | Decompose some composite motif into two separate submotifs |
getSeqFromUCSC | Get DNA sequences from UCSC genome database directly through... |
highlightMismatch | Highlight the mismatches of sequence(s) to some reference... |
kmer | Enumerate all k-mer sequences |
matchPEM | find binding sites within some GenomicRanges or DNA sequences... |
plotEnergyLogo | Visualize some energy matrix by plotting logo |
predictEnergy | Predict the binding energy of input sequences based on energy... |
predictEnergyMW | Predict the binding energy of input sequences based on energy... |
reverseComplement | Reverse some existing position energy matrix |
selectVariants | Select sequence variants based on the max number of... |
SeqToByte | Convert DNA sequences to binary code based on various... |
SeqToMethylByte | Convert DNA sequences to binary code only including... |
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