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@bramvds bramvds released this 27 Feb 17:38
· 180 commits to master since this release
0.10.0
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Learn about vigilant mode.

Updates:

  • Added a helper script scripts/arboreto_with_multiprocessing.py that runs the Arboreto GRN algorithms (GRNBoost2, GENIE3) without Dask for compatibility.
  • Initial support for the use of sparse expression matrices (applies only to the GRN step in the CLI currently). Using sparse matrices with the GRN step requires a patch to Arboreto (tmoerman/arboreto#20)
  • AUCell uses a random sampling of the expression matrix to break ties in the ranking step. The CLI parameter --seed or aucell function parameter seed uses a fixed seed for this step. The regulon thresholds also depend on random sampling in the binarization step (bimodality test: np.random.uniform), and the seed parameters apply here as well.
  • Fixed typo in regulon threshold labeling
  • Security patch: Bump bleach from 3.1.0 to 3.1.1.
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