Methods
The Division of Cancer Epigenomics offers a range of molecular biology and computational tools for understanding epigenomic (de)regulation.

Chromatin organization
Antibody-guided chromatin tagmentation (ACT-seq) enables the profiling of histone modifications and transcription factors.
Hi-ChIP profiles chromatin interactions coupled with a specific histone modification.
The assay for transposase-accessible chromatin with sequencing profiles open chromatin regions in the genome.
DNA methylation
Illuminas microarrays enable the profiling of DNA methylation of a defined subset of CpGs at high sample throughput.
(tagmentation-based) Whole-Genome Bisulfite Sequencing profiles the methylation state of nearly all CpG dinucleotides in the human genome. We also established a protocol working with very low levels of input DNA.
MoreEM-seq is an enzymatic alternative to WGBS.
Single cell/nucleus sequencing

Single-cell Targeted Analysis of the Methylome (scTAM-seq) profiles DNA methylation states of a subset of up to 1,000 CpGs in several thousand cells per experiment. It can be combined with the readout of surface proteins, somatic mutations, and a selected set of gene expression states. It also enables clonal tracing through somatic epimutations.
MoresnATAC-seq through 10x solution enables the profiling of open chromatin in single cells.
sRNA-seq through 10x solution enables the profiling of gene expression states in single cells.
Long read sequencing
Oxford nanopore sequencing enables the sequencing of long fragments of several thousand bases.
DiMeLo-seq profiles chromatin modification together with DNA methylation and stuctural variants across long genomic distances.
MoreComputational tools

RnBeads is an R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution. Supported assays include Infinium and EPIC microarrays and bisulfite sequencing protocols, and also MeDIP-seq and MBD-seq once the data have been preprocessed with DNA methylation level inference software. RnBeads implements an analysis workflow that is significantly more comprehensive than those of existing tools. It documents its results in a highly annotated and readable hypertext report, and it scales to the large sample sizes that are becoming the norm for DNA methylation analysis in human cohorts.
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MeDeCom is an R package for reference-free decomposition of heterogeneous DNA methylation profiles. It uses constrained matrix factorization enhanced by biologically-relevant constraints and a specially tailored regularization. See MeDeCom protocol for a more detailed description and an example analysis.
MorePyjacker detect enhancer hijacking events in a cohort of at least 10 samples profiled with WGS and RNA-seq. It does not require matched normals and can detect enhancer hijacking events occurring in only a single sample. Briefly, it looks for outlier high and monoallelic expression of a gene in a sample which has a breakpoint close to the gene.
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