- Garnet integration test case using FOXA1 ChIP-seq
- Correct formatting problems in example data wgEncodeRegDnaseClusteredV2.fasta.gz
- Fix bug when reading Garnet results in Forest
- Use relative paths for motif gifs in Garnet HTML output file
- Update sort order in Garnet output table
- Garnet uses balanced binary search tree to speed up the search for genes within peaks
- Change default values of arguments in Garnet's map_peaks_to_known_genes.py
- Remove conflicts between Forest edge noise and garnetBeta parameters
- Correctly query for whether prize nodes are in a directed network
- Use correct p-value or q-value to filter Garnet output
- Switch to msgsteiner-1.3 to fix bugs with directed edges and suboptimal forests
- BSD license
- Forest unit tests to assess the effects of w, beta, mu, and D
- Continuous integration testing with Travis CI
- Option to save plots from Garnet motif regression
- Write Forest objective function value of optimal forest to info file
- Add a Forest integration test
- Correct nondeterministic msgsteiner behavior
- Add additional example data sets and scripts
- Switch to Creative Commons Attribution-NonCommercial 4.0 International Public License
- Rename Forest configuration file parameter n to garnetBeta
- Add Forest configuration file parameter processes
- Correct error in negative prize score calculation
- Improve Garnet output file format
- Add Forest option to exclude terminals
- First release on PyPI.