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.

rustscenic

Rust + PyO3 reimplementation of the SCENIC+ single-cell regulatory-network pipeline. ATAC preproc, peak calling, GRN, AUCell, topics, cistarget, eRegulon — one pip install, no Java, no MACS2, no dask.

nordic

Network Oriented Repurposing of Drugs (NORDic): network identification / master regulator detection / drug effect simulator / drug repurposing

grnndata

Awesome GRN enhanced AnnData toolkit

regdiffusion

Diffusion model for gene regulatory network inference.

netzoopy-sponge

A package to generate prior gene regulatory networks.

netzoopy

Python implementation of netZoo

dysregnet

Inferring patient-specific regulatory alterations

cellnition

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

airqtl

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

normalisr

Normalisr Offers Robust Modelling of Associations Linearly In Single-cell RNA-seq

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

pyscorpion

Constructs cell-type-specific gene regulatory networks from single-cell RNA-sequencing data using the SCORPION algorithm, which aggregates cells into super-cells and applies PANDA to infer transcription factor-target regulatory relationships.