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

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...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics 2016-04, Vol.32 (8), p.1211-1213
Main Authors: Chiu, Tsu-Pei, Comoglio, Federico, Zhou, Tianyin, Yang, Lin, Paro, Renato, Rohs, Remo
Format: Article
Language:English
Subjects:
Applications Notes
Bioinformatics
Deoxyribonucleic acid
DNA
Encoding
Gene sequencing
Genome
Genomics
Graphical representations
HyperText Markup Language
Packages
Programming Languages
Software
Software packages
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. 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 data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btv735