Why We Built EpiNexus
Updated 3 October 2026 to match the current EpiNexus app.
Epigenomic experiments generate rich, complex data — ChIP-seq peaks, histone modification maps, super-enhancer landscapes. But for most wet lab researchers, turning raw FASTQ files into publication-ready figures means either learning command-line bioinformatics or waiting weeks for a collaborator.
We built EpiNexus to close that gap.
The problem
A typical ChIP-seq analysis involves a dozen tools: FastQC, Trimmomatic, Bowtie2, SAMtools, MACS2, DiffBind, ROSE, HOMER, deepTools — each with its own installation headaches, parameter choices, and output formats. Even experienced bioinformaticians spend days stitching these together.
For a biologist who just wants to know which enhancers changed between treatment and control, this is an unreasonable barrier.
Our approach
EpiNexus wraps the entire pipeline — from raw FASTQ trimming and read mapping through peak calling, quality control, genomic annotation, differential analysis, and super-enhancer detection — into a single web interface. You upload your files (or import published data from GEO, SRA or ENA), choose your genome and assay type, and click run.
No terminal. No scripts. No conda environments.
What you get
Every analysis produces interactive, publication-ready outputs:
- Volcano plots showing gained and lost peaks with gene labels
- Signal heatmaps across all your replicates
- Super-enhancer hockey stick plots ranked by signal
- Genomic annotation charts breaking down where your peaks land
- Downloadable tables ready for supplementary materials
Figures are interactive — hover for details — and the main ones export as SVG or PNG for your paper. Every run also records its tool versions and commands and writes a methods section you can adapt.
Who it's for
EpiNexus is built for wet lab researchers who generate epigenomic data but don't want to become bioinformaticians. If you can upload a file and click a button, you can run a full analysis.
We currently support ChIP-seq, CUT&Tag, CUT&RUN, ATAC-seq, and DNA methylation (WGBS and RRBS).
What's next
EpiNexus is now open as an invite-only pilot at app.epinexus.io. If you'd like an account, get in touch — we'd love to hear about your project.