DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.

ABSTRACT:

Unlabelled

DNAshapeR predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape features. The resulting feature matrices can be readily used as input of various machine learning software packages for further modeling studies.

Availability and implementation

The DNAshapeR software package was implemented in the statistical programming language R and is freely available through the Bioconductor project at https://www.bioconductor.org/packages/devel/bioc/html/DNAshapeR

SUBMITTER: Chiu TP 

PROVIDER: S-EPMC4824130 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature