01 Quality Control
~2 minChecks whether your data is high quality — read mapping, signal enrichment, fragment sizes, and library complexity.
When you click "Run Analysis", EpiNexus works through up to six analysis steps. You can watch the progress bar in real time. Some steps (like super-enhancers and integration) are optional and can be enabled in your run settings.
Checks whether your data is high quality — read mapping, signal enrichment, fragment sizes, and library complexity.
Labels each peak by where it sits in the genome (promoter, intron, intergenic, etc.) and finds the nearest gene.
Connects each enhancer or regulatory region to the gene(s) it most likely controls.
Compares two conditions (e.g. treated vs. control) to find which peaks gained or lost signal.
Combines multiple histone marks to classify regions as active, poised, bivalent, or repressed.
Identifies the large, high-signal regulatory regions that define cell identity and disease states. Enable this optional step in the run settings.
17 pre-configured genomes across all major model organisms. Add any other species via NCBI accession or your own reference files.
Homo sapiens
GRCh38 · GENCODE v46Homo sapiens
GRCh37 · GENCODE v46liftMus musculus
GRCm39 · GENCODE vM35Mus musculus
GRCm38 · GENCODE vM25Rattus norvegicus
mRatBN7.2 · UCSC ncbiRefSeqRattus norvegicus
Rnor_6.0 · UCSC ncbiRefSeqDanio rerio
GRCz11 · UCSC ncbiRefSeqDrosophila melanogaster
BDGP6 · UCSC ncbiRefSeqCaenorhabditis elegans
WBcel235 · UCSC ncbiRefSeqSaccharomyces cerevisiae
R64 · UCSC ncbiRefSeqMacaca mulatta
Mmul_10 · MacaqueGallus gallus
GRCg6a · ChickenXenopus laevis
v10.1 · FrogSus scrofa
Sscrofa11.1 · PigBos taurus
ARS-UCD1.2 · CowCanis lupus familiaris
UU_Cfam_GSD_1.0 · DogArabidopsis thaliana
TAIR10 · Ensembl Plants 62EpiNexus works with any organism that has a reference genome. Add genomes from NCBI (over 1 million assemblies) or provide your own FASTA and GTF files.
Any sequenced organism in the NCBI Assembly database
Custom assemblies, proprietary genomes, unpublished species
Pre-configured genomes use FASTA sequences from UCSC and gene annotations from GENCODE (human and mouse), UCSC ncbiRefSeq (other animals), or Ensembl Plants (Arabidopsis). All references use chr-prefixed chromosome naming for consistency. Custom genomes can be added with a single command via the NCBI datasets CLI or from local files.