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Orchid

Orchid

Orchid is a machine learning framework tool to manage, annotate, and analyze cancer mutations to support the knowledge of tumor genetic data. Example of usage: Sub-typing aggressive vs. non-aggressive prostate cancer using mutational profiles in tumor sequence data. NOTE: Orchid requires code or data under separate licenses or copyrights restricting the usage to non-commercial activities.

Topic

Oncology; Genetic variation; Machine learning; Nucleic acid structure analysis

Details

  • Operation: SNP annotation; Query and retrieval; Genetic variation analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: The MIT License
  • Cost: Free (See notes regarding data usage)
  • Version name: -
  • Maturity: Emerging
  • Credit: The National Institutes of Health (NIH), the UCSF Goldberg-Benioff Program in Cancer Translational Biology, Amazon Web Services, Microsoft Azure Web Services.
  • Contact: JWitte _at_ ucsf.edu
  • Collection: -

Publications

Cario CL, Witte JS "Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations." Bioinformatics 2018; 34(6):936-942 https://doi.org/10.1093/bioinformatics/btx709
PMID: 29106441
PMCID: PMC5860353


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