Desktop app for single-cell RNA-seq
Exona, the desktop app
Analyse single-cell RNA-seq data step by step, from quality control to marker genes, without a terminal. Every step is recorded and your data stays on your machine or your own server.
Why Exona
Built for biologists, not for terminals
Zero terminal setup
Exona installs and manages its own R and Python environment.
Your folder, no lock-in
Each project is a self-contained folder on your own disk.
Publication ready
Figures drawn with ggplot2 and saved as high-resolution PNG images, with cluster and UMAP plots at 300 DPI.
Analysis workflow
From raw counts to marker genes
A guided Seurat 5 analysis, one step at a time, with suggested cut-offs you can adjust.
Data import
10x Genomics Cell Ranger output (MEX or .h5); merge samples and add metadata.
Quality control
Genes, UMIs, mitochondrial and ribosomal content, with suggested cut-offs.
Processing
Normalization, variable genes and PCA with an elbow suggestion.
Clustering
Louvain clustering at several resolutions, explored on a UMAP.
Integration
Harmony, Seurat RPCA or CCA batch correction. In development.
Marker genes
Marker tables per cluster, exported as CSV, XLSX or RDS. In development.
On the roadmap: cell annotation, differential expression, enrichment and pathways.
In the app
See every decision you make
Quality control you can see
Choose filters with the data in front of you.
- Violin and density plots of QC metrics
- Cut-offs suggested from the median absolute deviation
- Before and after plots for every filter
Clusters and figures for your paper
Compare resolutions before you settle on one.
- UMAP by cluster, sample, condition or metadata
- Feature plots for the genes you care about
- PNG figures at 300 DPI
Remote compute
Your computer or your cluster
Exona runs on your computer. For bigger datasets, send the analysis to a Linux server through a compute plugin.
On your computer
Every step runs locally; the analysis engines listen only on your machine.
SSH compute plugin
From the in-app Plugin Manager. Uses your OpenSSH config, jump hosts and MFA; jobs survive a dropped connection.
Your cluster or HPC
A custom compute plugin can follow your cluster's setup and your IT rules.
About custom compute plugins
Provenance and methods
Every step on the record
A record that travels with your project
Each step's record stays with your self-contained project folder.
- Parameters and effective parameters of each step
- Software versions and timestamps
- Re-running a step invalidates the steps after it
- On the roadmap: a methods-text generator for your paper
For researchers and their IT
System requirements
Platforms
Windows
Windows 10 or 11 (x64), installer.
macOS
macOS 11 or later, Apple silicon and Intel.
Linux
Ubuntu 22.04 or 24.04 (x64), AppImage or deb.
For IT
- Display of 1280 × 800 or more, scales to 4K.
- First setup downloads the app's R and Python environment (internet needed once).
- Analysis stays on your machines or your server. No telemetry.
- Licensing is designed to never send dataset content and to work offline until the signed lease expires; your data is never locked.
Detailed hardware requirements are shared with your demo or quote.
See Exona on your own data
Tell us about your data and setup, and we will walk you through the workflow.