Epigenetics

Tutorials for the omicverse.epi (ov.epi) module — single-cell and bulk epigenomics, built as a thin wrapper over the epione toolkit. Every ov.epi function imports epione internally and delegates, so the familiar pp / tl / pl grammar now also covers chromatin accessibility and 3D genome organisation.

The single-cell ATAC tutorials (1–6) use small public 10x PBMC datasets that ov.epi.datasets downloads on demand, so they run end-to-end on a laptop CPU. The Hi-C tutorials (7–8) read local .cool / .scool files, and the bulk tutorials (9–10) cover the ChIP-seq upstream pipeline (FASTQ → peaks) and ATAC footprinting (provenance and accession noted in each notebook; the ChIP one fetches its reads from Zenodo, the footprint one reads a local TOBIAS reference).

• scATAC-seq preprocessing and quality control
• scATAC clustering, annotation and gene activity
• Transcription-factor motif activity with chromVAR
• Peak-to-gene linkage (multiome)
• Marker peaks and differential accessibility
• scRNA–scATAC integration and label transfer
• Bulk Hi-C — contact maps, compartments and TADs
• Single-cell Hi-C — imputation and cell-cycle embedding
• Bulk ChIP-seq upstream: FASTQ → peaks
• Bulk ATAC footprinting — TF activity from Tn5 cut profiles