SimiCPipeline
SimiCPipeline is the Python component of SimiC-Suite. It supports phenotype-specific gene regulatory network (GRN) inference from single-cell RNA-seq data and calculation of Regulon Activity Score (RAS) values for downstream interpretation.
SimiCPipeline builds on the SimiC framework for phenotype-aware regulatory network analysis. Please cite the original SimiC work when using SimiCPipeline where appropriate.
Tutorials
The tutorials below are local rendered copies of the Jupyter notebooks from the ML4BM-Lab/SimiCPipeline repository. They are rendered without executing code during website publication.
Full Pipeline Tutorial
Complete SimiCPipeline walkthrough, including initialization, parameter configuration, GRN inference, RAS calculation, and downstream result inspection.
Preprocessing Tutorial
Notebook covering data preparation steps for SimiCPipeline inputs, including expression data, transcription factor lists, and phenotype labels.
Visualization Tutorial
Notebook focused on inspecting and visualizing SimiCPipeline outputs after GRN inference and RAS calculation.
Helper Scripts
These reference scripts are copied from the SimiCPipeline notebook folder.