chromatin-accessibility

Pipeline for predicting ChIP-seq peaks in novel cell types using chromatin accessibility

ORACLE bulk ATAC-seq pipeline (Snakemake + conda): FASTQ/SRA to differential chromatin accessibility, peak annotation, TF motif enrichment & footprinting; multi-species, MultiQC.

Michael Vinyard's utilities

ORACLE single-cell ATAC-seq pipeline (Snakemake): 10x fragments to QC/doublets, LSI clustering, MACS3 peaks & differential accessibility, chromVAR/TOBIAS motifs, Cicero co-accessibility & trajectories.

ATAC-seq pipeline

A hands-on scaffold for processing single-cell ATAC-seq from fragments to a cell-by-peak matrix, with honest notes on sparsity.

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

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.

Mutation-to-epigenome origin analysis with benchmark workflows and result summaries

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