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Bioinformatics. 2016 Apr 15;32(8):1211-3. doi: 10.1093/bioinformatics/btv735. Epub 2015 Dec 14.

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

Author information

1
Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
2
Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland and.
3
Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland and Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.

Abstract

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.html and at the GitHub developer site, http://tsupeichiu.github.io/DNAshapeR/ CONTACT: rohs@usc.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26668005
PMCID:
PMC4824130
DOI:
10.1093/bioinformatics/btv735
[Indexed for MEDLINE]
Free PMC Article

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