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DNAshapeR

DNAshapeR is a R/BioConductor package for DNA shape prediction and feature encoding.

The latest (devel) version of DNAshapeR requires R >3.2.2 and can be installed from this GitHub repository with:

 library(devtools)
 install_github(repo = "TsuPeiChiu/DNAshapeR", build_vignettes = TRUE)

For more information, package vignette and documentation, please visit http://tsupeichiu.github.io/DNAshapeR/

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Version

Version

1.0.2

License

GPL-2

Maintainer

TsuPei Chiu

Last Published

February 15th, 2017

Functions in DNAshapeR (1.0.2)

normalize

Min-Max normalization
readShape

Read (parse) DNA shape predictions
heatShape

Plot heatmap of DNA shape features
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.
plotShape

Plot metaprofiles of DNA shape features
DNAshapeR-package

DNAshapeR package for high-throughput prediction of DNA shape features
getShape

Predict DNA shape from a FASTA file
encodeKMerSeq

Encode k-mer DNA sequence features
normalizeShape

Normalize n-st order shape features
trackShape

Plot track view of DNA shape 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.