Getting Started

Everything you need to install GeneCircuitry and run your first analysis.

Page What you’ll find
Installation Four install methods, optional dependency groups, verification
Quick Start CLI and Python API walkthroughs, expected output structure

What is GeneCircuitry?

GeneCircuitry is a Python package for transcriptional regulatory network (TRN) analysis of single-cell RNA-seq data. It combines three established tools into a single checkpointed pipeline:

Tool Role
Scanpy Quality control, normalization, dimensionality reduction, clustering
CellOracle Gene regulatory network (GRN) inference per cluster
Hotspot Identification of spatially autocorrelated gene modules

The pipeline is built around the PipelineController class, which manages checkpoints, logging, parallelism, and per-cluster stratification so you can run analyses reproducibly and resume interrupted jobs automatically.

Minimum requirements

  • Python ≥ 3.9
  • An AnnData .h5ad file (or use the bundled PBMC 3k example)

CellOracle and Hotspot are optional — the core pipeline runs without them.

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