SimiC-Suite

A reproducible framework for phenotype-specific gene regulatory network analysis from single-cell RNA-seq data.

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

SimiC-Suite graphical abstract

Overview

SimiC-Suite is a software suite for phenotype-specific gene regulatory network (GRN) analysis from single-cell RNA-seq data. It brings together complementary tools for GRN inference, Regulon Activity Score (RAS) calculation, and downstream assessment and visualization.

Suite Components

SimiCPipeline

Python package for phenotype-specific GRN inference and Regulon Activity Score (RAS) calculation.

Feature Description
Ecosystem Python
Role Upstream inference and RAS calculation.
Tutorials Rendered Jupyter notebooks from the package repository.

Open SimiCPipeline

SimiCviz

R / Bioconductor package for tool-agnostic assessment and visualization of GRN outputs.

Feature Description
Ecosystem R / Bioconductor
Role Downstream assessment, visualization, and reporting.
Tutorials Local copy of the rendered package vignette.

Open SimiCviz

Repositories