Epigenomics Analysis Platform

From ChIP-seq peaks to super-enhancer maps, DNA methylation to chromatin accessibility — run publication-ready epigenomic analyses 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, BAM, or BED files directly in the browser.

ChIP-seq, CUT&Tag, ATAC-seq

FASTQ.gz, BAM, BED, narrowPeak

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

Every module designed for histone mark analysis, from QC to super-enhancer calling.

Peak Calling & Annotation

Automatically detect enriched regions in your ChIP-seq data and see which genes and genomic features they overlap — promoters, enhancers, introns, and more.

Histone Mark Analysis

Analyse H3K27ac, H3K27me3, H3K4me1, and other marks side by side. EpiNexus classifies chromatin states (active, poised, bivalent, repressed) for you.

Super-Enhancer Detection

Identify the large, highly active regulatory regions that drive cell identity. EpiNexus uses the ROSE algorithm 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 activating and repressive marks across conditions to discover bivalent domains, poised enhancers, and regions that switch chromatin state.

Differential Analysis

Compare two conditions (e.g. treated vs. untreated) to find peaks that gain or lose signal. Results include interactive volcano plots and downloadable tables.

View All Features →