software

Open source software from the GenomeDataLab:

  • HyperClust by David Mas-Ponte. https://github.com/davidmasp/hyperclust
    • A statistical framework to detect clustered mutations in genomes, while accounting for mutation rate heterogenety and for estimated timing of the mutations.
  • BioPanPipe by Daniel Ortiz-Martinez. https://daormar.github.io/bio-panpipe/
    • A genomics pipeline implementing a variety of tools for variant calling, including point mutations, indels, copy number changes and LOH, MSI analysis and structural variants. Additionally, tools for download from genomics databases.
  • FastRandomForest2 (beta) by Jordi Piqué Sellés. https://github.com/GenomeDataScience/FastRandomForest
    • A re-implementation of the Random Forest classifier (RF) for the Weka machine learning environment, bringing massive speed and memory use improvements.

"An approximate answer to the right problem is worth a good deal more than an exact answer to an approximate problem." -- John Tukey