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 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
- (since 0.9.18) In the modules_from_adjacencies function, the default value of
rho_mask_dropoutsis 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 (