What's Changed
- Bugfix: fixed bug in generation of simulated count profiles for calculating complementary log-likelihood ratio test (cLRT) background distributions
- Test False WGMs: implemented cLRTs for unsupported ("False") WGMs in addition to supported ("True") WGMs
- Benjamini-Hochberg FDR correction: implemented Benjamini-Hochberg FDR correction of cLRT p-values
- Test for a single WGM: the cLRT workflow is executed only on a single WGM, instead of on all WGMs listed in the input file.
- Remove consecutive WGMs: added code for handling the removal of one WGM on a branch containing several (max 3) WGMs
- CLI implementation: the cLRT workflow is available as a JAVA command line tool
- Minor: code efficiency improvements
Developed by Cecilia Sensalari and Dr. Steven Maere based on v2.0.0-dev by Setareh Tasdighian (in preprint, 2025)