title: DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
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.
  
  
  
  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.
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Tsu-Pei
authors.initials: TP
authors.lastname: Chiu
authors.affiliation: Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland and.
authors.forename: Federico
authors.initials: F
authors.lastname: Comoglio
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Tianyin
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: Renato
authors.initials: R
authors.lastname: Paro
authors.affiliation: Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: Remo
authors.initials: R
authors.lastname: Rohs
mesh_terms: D004247:DNA; D016678:Genome; D023281:Genomics; D011381:Programming Languages; D012984:Software
chemical_list: D004247:DNA