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 and PyO3 implementation of SCENIC-style regulatory-network analysis. Includes GRN, AUCell, topics, cistarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly. Installs without dask, Java, or CUDA.

nordic

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

normalisr

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

regdiffusion

Diffusion model for gene regulatory network inference.

grnndata

Awesome GRN enhanced AnnData toolkit

netzoopy-sponge

Python package to generate prior gene regulatory networks.

netzoopy

netZooPy is a network biology package implemented in Python.

dysregnet

Inferring patient-specific regulatory alterations

airqtl

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

cellnition

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

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.