flashscenic

flashscenic#

GPU-accelerated SCENIC workflow for gene regulatory network analysis.

flashscenic replaces the bottleneck steps in the SCENIC pipeline with GPU-powered alternatives, achieving seconds instead of hours for large-scale single-cell analyses.

Key Features#

  • One-call pipeline: run_flashscenic() handles GRN inference through AUCell scoring

  • Automatic data downloads: TF lists, ranking databases, and motif annotations

  • GPU-accelerated: All core operations use vectorized PyTorch

  • Scalable: Handles 20,000 genes and millions of cells

  • Multi-species: Human, mouse, and drosophila support

Getting Started#

import flashscenic as fs

result = fs.run_flashscenic(exp_matrix, gene_names, species='human')
auc_scores = result['auc_scores']  # (n_cells, n_regulons)

User Guide

Reference

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