SimiC-Suite

Overview

SimiC-Suite is an open-source software framework for inferring and studying phenotype-specific gene regulatory networks (GRNs) from single-cell RNA-seq data. The suite combines robust network inference, regulon activity score (RAS) calculation, and comprehensive visualization tools into a unified workflow for exploring regulatory mechanisms across biological conditions.

Designed for reproducible and interpretable GRN analysis, SimiC-Suite supports researchers from data preprocessing and GRN inference through downstream assessment, visualization, and reporting.

Graphical abstract summarizing the SimiC-Suite workflow from single-cell RNA-seq inputs through SimiCPipeline, SimiCviz, and downstream reporting.

SimiC-Suite graphical abstract

Suite Components

SimiCPipeline

Python package for phenotype-specific GRN inference, RAS calculation and downstream assessment and visualization of GRN outputs.

Feature Description
Ecosystem Python
Role Upstream inference and RAS calculation. Downstream assessment and visualization workflows described.
Tutorials Jupyter notebooks from the package repository.

Open SimiCPipeline

SimiCviz

R package for tool-agnostic RAS calculation, assessment and visualization of GRN outputs.

Feature Description
Ecosystem R
Role RAS calculation, downstream assessment, visualization, and reporting.
Tutorials Local copy of the rendered package vignette.

Open SimiCviz

Repositories