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.

Modular single-cell transcriptomics pipelines for Alzheimer’s disease, integrating R and Python workflows.

scRNA-seq analysis of tissue-resident memory T cells (TRM): Scanpy pipeline, pySCENIC GRN inference, basin stability modeling, and Cell Systems manuscript

Single-Cell Atlas Builder is a modular platform for processing, integrating, and visualizing single-cell RNA-seq datasets. It combines FastAPI, Scanpy, and CellTypist for efficient analysis, with optional LLM-powered summaries for cluster and pathway interpretation.

Pipelines for single-cell data in Nextflow DSL2. Updated to run SCENIC single- and multi-run workflows with feather v2 cisTarget v10 resources