pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
-BugFixes: #100 and #51.
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. Since this is likely to change the final output regulons slightly, warnings have been added to the logging system. The cli version has an additional option to turn dropout masking back on (--mask_dropouts).
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. Since this is likely to change the final output regulons slightly, warnings have been added to the logging system. The cli version has an additional option to turn dropout masking back on (--mask_dropouts).
BugFix: minor bugfix in calculation of Regulon Specificity Score (RSS).
New features: multiprocessing support for the binarization function.
BugFix: CLI grn - output of list of adjacencies is TSV or CSV (default) based on provided file extension.
New functionality: support for multiple embeddings then exporting to loom file.