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.
“To invent, you need a good imagination and a pile of junk.” ― Thomas A. Edison