Genewalk

Latest version: v1.6.3

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1.2.0

- Support for human Ensembl IDs in gene lists
- Support for human and mouse Entrez IDs in gene lists
- Upgrade to PathwayCommons v12
- All input genes are now present in the GeneWalk network as long as they have GO annotations, irrespective of their gene-gene connectivity (previously only genes that had other direct gene connections were included in the network).
- Fix the calculation of the 95% confidence interval around mean p-adjust (does not affect the mean value reported with prior versions).
- In case of numerical underflow for p values, a default minimum of 1e-16 is set.
- Add `--version` argument to CLI to print version
- Add `--random_seed` argument to CLI to reproduce prior results
- Compatibility updates to support networkx 2.4+
- Automated testing on TravisCI

1.1.0

- Improved parallelization scheme implemented in `genewalk.deepwalk`, used when `nproc` > 1
- Default number of repeats (`nreps_graph`, `nreps_null`) set to 3
- Extended README with documentation, funding and citation

1.0.0

Initial release of GeneWalk

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