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- Software type:
- Restrictions to use:
- Output data:
- Minor groove width, helix twist, propeller twist and Roll can then be visualized in the form of plots, heat maps or genome browser tracks or used for the assembly of feature vectors of user-defined combinations of k-mer and shape features.
- Programming languages:
- DNAshapeR version 1.0
- R version 3.2.2 or later
- Command line interface
- Input data:
- The input data can be either nucleotide sequence(s) in FASTA file format or genomic intervals, provided by the user in BED format or derived from public databases.
- Operating system:
- Unix/Linux, Mac OS, Windows
- Computer skills:
- Documentation: http://rohslab.cmb.usc.edu/Documents/DNAshapeR_document.pdf
- Remo Rohs <rohs at usc.edu>
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(Chiu et al., 2015) DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. Bioinformatics.
Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA; Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland; Faculty of Science, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
This work was supported by the NIH (R01GM106056, R01HG003008 in part, and U01GM103804).