archr

Analysis code for Amrute, Luo et al., Nature (2024): CITE-seq, single-nucleus multiome and spatial transcriptomics of human heart failure identifying FAP+/POSTN+ fibroblasts and IL-1b-driven immune-fibroblast communication.

Chromatin accessibility analysis of spaceflight (NASA) mouse brains using ArchR (Master's Thesis Project)

multiomics OCT4

archR: Identifying promoter sequence architectures de novo using NMF

WDLized ArchR

Single-cell ATAC-seq analysis of human brain cortex cells using ArchR, Harmony, motif analysis and peak-to-gene linkage.

Annotated guide for running ArchR single-cell ATAC-seq analysis on a bioHPC cluster, with troubleshooting tips and commentary

An R/ArchR pipeline for single-cell ATAC-seq analysis, producing accessibility embeddings, visualizations, and a report-style set of results with renv-based environment management.