Version 2 of facets-suite replaces prior version and is a complete structural revamp.
The essential functionality remains unchanged. This new version of the facets-suite repository contains an R package (facetsSuite) which contains standalone functions that individual wrapper scripts use for the core usage cases. The motivation for these changes was to remove code redundancy and improve stability and reproducibility. Additionally, this new repository aims to better document both usage and functionality.
Old releases remain accessible through the release page: https://github.com/mskcc/facets-suite/releases