Epigenomics Analysis Platform

EpiNexus is a web platform for analysing epigenomic sequencing data — ChIP-seq, CUT&Tag, CUT&RUN, ATAC-seq and DNA methylation. Run publication-ready analyses, from raw reads to super-enhancer maps, without writing a single line of code: upload your files, click run, get results.

Get Started See What It Does

Upload Your Data

Drag and drop your FASTQ or BAM files in the browser, or import public data straight from GEO, SRA or ENA.

ChIP-seq, CUT&Tag, CUT&RUN, ATAC-seq, DNA methylation
FASTQ.gz, or BAM with its peak files
Choose your reference genome

Click Run

EpiNexus runs a full pipeline — QC, mapping, peak calling, annotation, differential analysis, and more.

Quality control & read mapping
Peak calling & annotation
Differential & super-enhancers

Explore Results

Interactive volcano plots, heatmaps, super-enhancer rankings — ready for your paper.

Built for Epigenomics

Modules for histone marks, transcription factors, chromatin accessibility and DNA methylation, from QC to super-enhancer calling.

Peak Calling & Annotation

Automatically detect enriched regions in your data and see which genes and genomic features they overlap — promoters, exons, introns, and distal regions.

Histone Mark Analysis

Analyse H3K27ac, H3K27me3, H3K4me1, and other marks side by side. Each mark is called with the right peak shape — narrow or broad — and input or IgG controls are used as background.

Super-Enhancer Detection

Identify the large, highly active regulatory regions that drive cell identity. EpiNexus runs the ROSE algorithm on H3K27ac, MED1 or BRD4 data and highlights your top-ranked super-enhancers.

Quality Control

Instantly see whether your data is high quality. Get clear metrics on signal enrichment, fragment sizes, library complexity, and more — all in one report.

Multi-Mark Integration

Compare how H3K27ac and H3K27me3 change between conditions, gene by gene: activated, repressed, both gained, poised, or stable — with a diagram of how each mark moved.

Differential Analysis

Compare conditions (e.g. treated vs. untreated) to find peaks that gain or lose signal, with DESeq2 statistics (csaw for broad marks), interactive volcano plots and downloadable tables.

View All Features →