High-throughput prediction of DNA shape features

Documentation for package ‘DNAshapeR’ version 1.21.0

DNAshapeR-package	DNAshapeR package for high-throughput prediction of DNA shape features
convertMethFile	Convert fasta file to methylated file format
encodeKmerHbond	encode Hbond
encodeKMerSeq	Encode k-mer DNA sequence features
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