Solutions for every assay in one workflow editor.
Drop in the vendor output, connect nodes, run. Oreumics ships 119 nodes and 33 templates for single-cell, spatial, bulk RNA-seq, ATAC-seq and DNA methylation — all on the same canvas, with the same parameter panel, workspaces, AI Copilot, Figure Canvas and reports.
Single-cell RNA-seq
From raw counts to an annotated cell atlas
Live QC Workspace, Leiden / Louvain / K-Means, four annotation methods with a concordance check, CellRank fate analysis, LIANA and CellPhoneDB communication.
66
Nodes
8
Loaders
20
Templates
Spatial transcriptomics
Visium, Visium HD, Xenium, MERSCOPE and CosMx on one canvas
Native loaders, an interactive viewer with lasso, box and polygon selection, BANKSY domains, cellular neighborhoods and the squidpy statistics.
50
Nodes
10
Loaders
4
Templates
Bulk RNA-seq
featureCounts to PyDESeq2 to GSEA, without R
Kallisto, Salmon, featureCounts and STAR counts; CPM / TMM / DESeq2 / VST; PyDESeq2 differential expression; GSEA / ORA and pathway activity.
19
Nodes
4
Loaders
3
Templates
ATAC-seq
Fragments to peaks to motifs
Fragments, peak matrices or Cell Ranger ATAC MEX; TSS / FRiP QC, peak calling, LSI, differential accessibility and pyJASPAR motif enrichment.
17
Nodes
4
Loaders
2
Templates
DNA methylation
IDAT to DMP, DMR and GOmeth
mepylome IDAT loading with raw-signal QC, quantile normalisation, DMP / DMR, feature enrichment and CpG-bias-corrected GOmeth for 450K, EPIC v1 / v2 and Mouse arrays.
19
Nodes
3
Loaders
4
Templates
Shared vocabulary
10 nodes appear in three or more of these views.
Loading, metadata, subsetting, the kNN graph, embedding, clustering and export are the same nodes everywhere, so a second modality is a new view of a library you already know.
Stop stitching together a different tool for every modality.
One UI, one mental model
Every modality uses the same node graph, the same parameter panel and the same QC, Embedding and Visualization Workspaces. The Node Library switches view per modality; the nodes underneath are shared. Learn it once.
One Copilot, one MCP server
The AI Copilot reads the same node catalog for every modality, proposes action plans you apply or undo, and runs approved plans with Approve & Run. The same catalog is exposed to Claude Desktop, Claude Code and the ChatGPT desktop app through the built-in MCP server.
One project, many workflows
A .bioflow project holds several workflow tabs, so an scRNA-seq run and a methylation run can live side by side and open together. The Figure Canvas lays out finished figures for a composite panel, and reports come with auto-generated Methods text.
End matter
Pick your modality. Start free.
Free during the beta — access by admin-issued Beta Access ticket. Windows 10/11, 64-bit. No credit card required.