Gene Regulatory Network Python Packages

pyscenic

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.

nordic

Network-Oriented Repurposing of Drugs Python Package

rustscenic

Fast, memory-efficient tools for studying gene regulation in single-cell data, built with Rust and Python.

netzoopy-sponge

Python package to generate prior gene regulatory networks.

pyscorpion

Single Cell Oriented Reconstruction of PANDA-based Individually Optimized Networks

grnndata

Awesome GRN enhanced AnnData toolkit

regdiffusion

Diffusion model for gene regulatory network inference.

normalisr

Causal inference, differential expression, and co-expression for scRNA-seq

airqtl

Single-cell eQTL mapping and causal gene regulatory network inference at high efficiency and accuracy

netzoopy

netZooPy is a network biology package implemented in Python.

cytorete

Cell-type-resolved gene regulatory network inference from single-cell data.

cellnition

Analyze gene regulatory networks (GRNs) via Network Finite State Machines (NFSMs).

dysregnet

Inferring patient-specific regulatory alterations

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis