ChIP-seq

Make enhancer analyses gene-aware, but not gene-blind

A practical framework for integrating enhancer states, chromatin signal and gene expression without pretending that nearest gene assignment solves everything.

Use pseudoreplicates to make peak sets less fragile

A generic strategy for using pseudoreplicates and IDR-like thinking to build more robust ChIP-seq and ATAC-seq peak sets.

A QC checklist before trusting ChIP-seq or ATAC-seq peaks

A compact checklist for deciding whether ChIP-seq or ATAC-seq peak calls are biologically interpretable.

Epigenomic data analysis with UNIX and R

Hands-on training in ChIP-seq, ATAC-seq and MNase-seq analysis, from sequencing quality control to peak calling, normalization and functional interpretation.