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 single-cell regulatory-network analysis. GRN, AUCell, topics, cisTarget, peak calling, cell QC, enhancer-gene links, and eRegulon assembly in one pip install.

nordic

Network-Oriented Repurposing of Drugs Python Package

regdiffusion

Diffusion model for gene regulatory network inference.

grnndata

Awesome GRN enhanced AnnData toolkit

netzoopy-sponge

A package to generate prior gene regulatory networks.

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).

netzoopy

netZooPy is a network biology package implemented in Python.

dysregnet

Inferring patient-specific regulatory alterations

normalisr

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