Everything you need to go from raw ChIP-seq data to publication-ready figures — all from your browser.
Automatically find enriched regions in your data. Supports both sharp (e.g. transcription factor) and broad (e.g. H3K27me3) peak shapes, with built-in replicate consistency scoring.
See exactly where each peak lands — is it at a promoter, in an intron, near an enhancer, or out in an intergenic region? Every peak is linked to its nearest gene automatically.
Compare conditions (e.g. treated vs. control) to find peaks that gain or lose signal. Uses PyDESeq2 statistics under the hood, with clear volcano plots and result tables.
Discover the large, highly active regulatory regions that drive cell identity. EpiNexus stitches nearby peaks, ranks them by signal, and separates super-enhancers from typical enhancers.
Combine activating marks (e.g. H3K27ac) with repressive marks (e.g. H3K27me3) to see the full chromatin landscape. Identify active, poised, bivalent, and repressed regions at a glance.
Find out which genes each enhancer or regulatory region likely controls. Uses distance-based linking by default, with optional ABC model and correlation-based methods.
Before you even start analysis, EpiNexus checks your data: how well reads mapped, signal-to-noise ratio, fragment sizes, and library complexity — all summarised in a clear report.
Drag and drop your FASTQ, BAM, or peak files right in the browser. All files are organised by project, and results are stored alongside your uploads for easy access.
EpiNexus validates your data at each step and gives clear error messages if something goes wrong. Re-run with corrected settings or files — your uploads are preserved.