DNAshapeR

"DNAshapeR" is an R package designed to predict DNA shape features from genomic sequencing data in a high-throughput and ultra-fast manner. This tool can process both nucleotide sequences and genomic coordinates as input, allowing users to generate various graphical representations for both visualization and subsequent analysis.

DNAshapeR stands out by its capability to encode DNA sequences and shape features into customizable combinations of k-mer and DNA shape features, creating feature matrices. These matrices are compatible with numerous machine-learning software packages, facilitating advanced modeling studies that can uncover novel insights into DNA structure and function.

Topic

DNA;Structure prediction

Detail

  • Operation: DNA structure prediction

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.30.0

  • Credit: NIH, NSF, Alfred P. Sloan Foundation.

  • Input: -

  • Output: -

  • Contact: Tsu-Pei Chiu tsupeich@usc.edu

  • Collection: -

  • Maturity: Stable

Publications

  • DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding.
  • Chiu TP, et al. DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. 2016; 32:1211-3. doi: 10.1093/bioinformatics/btv735
  • https://doi.org/10.1093/bioinformatics/btv735
  • PMID: 26668005
  • PMC: PMC4824130

Download and documentation

< Back to DB search