Release Notes

0.10.2 | 2020-06-05

  • Bugfix for CLI grn step

0.10.1 | 2020-05-17

  • CLI: file compression (optionally) enabled for intermediate files for the major steps: grn (adjacencies matrix), ctx (regulons), and aucell (auc matrix). Compression is used when the file name argument has a .gz ending.

0.10.0 | 2020-02-27

  • Added a helper script arboreto_with_multiprocessing.py that runs the Arboreto GRN algorithms (GRNBoost2, GENIE3) without Dask for compatibility.
  • Ability to set a fixed seed in both the AUCell step and in the calculation of regulon thresholds (CLI parameter --seed; aucell function parameter seed).
  • (since 0.9.18) In the modules_from_adjacencies function, the default value of rho_mask_dropouts is changed to False. This now matches the behavior of the R version of SCENIC. The cli version has an additional option to turn dropout masking back on (--mask_dropouts).