Faster, lower-memory Rust rewrite of the SCENIC and SCENIC+ analysis stack: GRN, AUCell, cisTarget, topics, peak-to-gene links, and eRegulons.
Modular single-cell transcriptomics pipelines for Alzheimer’s disease, integrating R and Python workflows.
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.
scRNA-seq analysis of tissue-resident memory T cells (TRM): Scanpy pipeline, pySCENIC GRN inference, basin stability modeling, and Cell Systems manuscript
Pipelines for single-cell data in Nextflow DSL2. Updated to run SCENIC single- and multi-run workflows with feather v2 cisTarget v10 resources
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