Methods
- ACT-seq
- Hi-ChIP
- ATAC-seq
- llumina EPIC and EPIC.v2 arrays
- EM-seq
- (tagmentation-based) WGBS (doi.org/10.1007/978-1-4939-9151-8_10)
- scTAM-seq (doi.org/10.1186/s13059-022-02796-7; doi.org/10.1038/s41586-025-09041-8)
- snATAC-seq
- scRNA-seq
- Oxford nanopore sequencing
- DiMeLo-seq (doi.org/10.1038/s41592-022-01475-6)
- DNA methylation: RnBeads (rnbeads.org) (doi.org/10.1038/nmeth.3115; doi.org/10.1038/s41596-020-0369-6)
- Deconvolution of DNA methylation: MeDeCom (https://epigenomics.dkfz.de/DecompProtocol/), doi.org/10.1186/s13059-017-1182-6, doi.org/10.1038/s41596-020-0369-6
- Enhancer Hijacking: pyjacker (doi.org/10.1158/2643-3230.BCD-24-0278)
- Epigenetic heterogeneity: epiCHAOS (doi.org/10.1186/s13059-024-03446-w)