Release Notes

0.10.3 | 2020-07-15

  • Integrate arboreto multiprocessing script into pySCENIC CLI
  • Skip modules with zero db overlap in cisTarget step
  • Additional error message if regulons file is empty
  • Additional error if there is a mismatch between the genes present in the GRN and the expression matrix
  • Fixed bug in motif url construciton when running without pruning

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 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).