Introduction

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.eduSupplementary data are available at Bioinformatics online.

Publications

  1. DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
    Cite this
    Chiu TP, Comoglio F, Zhou T, Yang L, Paro R, Rohs R, 2016-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Tsu-Pei Chiu
    Developer

    Molecular and Computational Biology Program, Departments of Biological Sciences, United States of America

  2. Federico Comoglio
    Developer

    Department of Biosystems Science and Engineering, ETH Zürich, Switzerland

  3. Tianyin Zhou
    Developer

    Molecular and Computational Biology Program, Departments of Biological Sciences, United States of America

  4. Lin Yang
    Developer

    Molecular and Computational Biology Program, Departments of Biological Sciences, United States of America

  5. Renato Paro
    Developer

    Department of Biosystems Science and Engineering, ETH Zürich, Switzerland

  6. Remo Rohs
    Investigator

    Molecular and Computational Biology Program, Departments of Biological Sciences, United States of America

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Summary
AccessionBT001085
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByRemo Rohs