Setty Lab @ Fred Hutch

Differential abundance and gene expression in single-cell data

Non-parametric density inference for single-cell analysis.

Claude Code skills for effective HPC usage.

Composable spatial and cell-state smoothing of gene signatures for single-cell and spatial transcriptomics

Snakemake pipeline for scATAC metacell utilities such as primed and lineage specific scores, chromVAR, in-silico ChIP

A statistical framework for identifying desynchronized cell states and their driver genes/regulatory elements from paired single-cell RNA and ATAC data.

An R package to convert SingeCellExperiment and Seurat objects into anndata as comprehensively as possible.

benchmarkDA repo for Kompot