DNAshapeR-package       DNAshapeR package for high-throughput
                        prediction of DNA shape features
convertMethFile         Convert fasta file to methylated file format
encodeKMerSeq           Encode k-mer DNA sequence features
encodeKmerHbond         encode Hbond
encodeNstOrderShape     Encode n-st order shape features DNAshapeR can
                        be used to generate feature vectors for a
                        user-defined model. The model can be a shape
                        model. There are four structural parameters
                        including MGW, Roll, ProT and HelT. The second
                        order shape features are product terms of
                        values for the same category of shape features
                        at adjacent positions.
encodeSeqShape          Encode k-mer DNA sequence and n-th order DNA
                        Shape features
getFasta                Extract fasta sequence given a set of genomic
                        intervals and a reference genome.
getShape                Predict DNA shape from a FASTA file
heatShape               Plot heatmap of DNA shape features
normalize               Min-Max normalization
normalizeShape          Normalize n-st order shape features
plotShape               Plot metaprofiles of DNA shape features
readNonStandardFastaFile
                        Read the position fasta file
readShape               Read (parse) DNA shape predictions
trackShape              Plot track view of DNA shape features
