Drop in raw data. Wire up nodes. Ship figures.
Oreumics turns 119 analysis steps into a visual graph on a Windows desktop. Drag a loader onto the canvas, branch into trajectories, spatial statistics or motifs, and walk the same canvas to a PDF report — with an AI Copilot that can edit the graph and an agent that runs it, step by step, in front of you.
scRNA-seq · Spatial · Bulk RNA-seq · Methylation · ATAC-seq. Every node computes locally; the app signs you in at launch.
One canvas. Five stages. Any modality.
Every analysis path — single-cell, spatial, bulk RNA-seq, ATAC-seq, methylation — walks the same five stages on the same canvas, with the same property panel and the same workspaces. The nodes differ; the way you work does not.
- 01
Load
22 loaders. H5AD, 10x H5 and MTX, CSV/TSV, Loom, Velocyto and STARsolo for single-cell; Visium, Visium HD, Xenium, MERSCOPE, CosMx and transcript tables for spatial; featureCounts, Kallisto and Salmon for bulk; IDAT and beta matrices for methylation; fragments and peak matrices for ATAC. Merge Cell Meta attaches a sample sheet.
- 02
QC
The Quality Control node opens a QC Workspace: MAD-based threshold recommendations, a Raw Data Mode for unfiltered droplets, and thresholds you move live without re-running. Scrublet flags doublets. Bulk QC, Methyl QC, ATAC QC and Spatial Density QC cover the other modalities.
- 03
Analyse
PCA, Harmony, neighbors, UMAP and t-SNE; Leiden or Louvain community detection on the kNN graph, or K-Means with a fixed number of clusters on the embedding plus K-Means; DEG, Enrichr and GSEA; 3 activity nodes; 4 annotation nodes; CellPhoneDB and LIANA; PAGA, DPT, scvelo and CellRank; squidpy spatial statistics, BANKSY domains and cellular neighborhoods; PyDESeq2; DMP, DMR and GOmeth; LSI and JASPAR motifs. Change one parameter and only the downstream nodes re-run.
- 04
Visualise
18 plot nodes draw 93 plot types. Each opens a Visualization Workspace with the same five sections, and every finished figure lands in the Figure Canvas gallery for layout, annotation and PNG/SVG/PDF export. The raw data behind any figure exports as CSV with an .LLM_README.md.
- 05
Report
The report outline is detected from your graph, you set the emphasis in a short chat, and Oreumics writes HTML or PDF. A Methods paragraph is generated from the nodes and parameters you actually ran, and project export carries run receipts and an RO-Crate.
Everything in the app, indexed.
Each card links to the page that describes the feature as it ships in v0.25.0.
Interactive views that open from a node card and change the figure or the data without re-running the pipeline.
QC Workspace
Set thresholds on the real distributions, then apply them once.
- MAD-based recommendations
- Raw Data Mode for unfiltered droplets
- Live thresholds — no pipeline re-run
Visualization Workspace
One vocabulary of controls shared by every plot node.
- Plot · Titles & Labels · Axes · Legend · Figure & Export
- Legend placement grid, group colours, group renaming
- Re-generate the figure without re-running the analysis
Figure Canvas
Every finished figure in one gallery, laid out by hand.
- Free layout, crop, text and arrow annotations
- PNG, SVG and PDF export
- Transparent background toggle
ObsInspector Workspace
Browse and tidy cell metadata before it drives an analysis.
- Per-column summaries and value counts
- Drop, rename and convert dtypes
- Preview before the node runs
Reports
From graph to HTML or PDF in three steps.
- Outline detected from the workflow
- Emphasis chat
- Methods text generated from your parameters
Node Catalog
119 nodes in 14 categories, organised by modality.
- scRNA-seq, Spatial, Bulk RNA-seq, Methylation, ATAC-seq
- Pipeline order, as in the app’s Node Library
- Every node linked to its parameter reference
Optional AI that reads node names, parameters and small summaries — never a matrix — and a receipt for every run so nothing has to be taken on trust.
AI Copilot
Chat that reads your data and edits your graph.
- OpenAI, Anthropic or Gemini — bring your own key
- 84 read tools, including which resources are installed
- Action plans with Apply and one-step Undo
AI Agent & MCP
Approve once; the agent runs and verifies each step on your canvas.
- Approval gate, step budget, Stop at any time
- Re-plans when a verification fails
- Connect Claude Desktop, Claude Code or the Codex app over MCP
Provenance
Every run leaves a receipt.
- Parameters, seed and determinism class per node
- RO-Crate inside the project export
- Methods paragraph written from the receipts
The parts of the app that hold a project together: the canvas, the templates, the resources and the memory guard.
Canvas, tabs and branches
Several workflows and Figure Canvases side by side, in split panes.
- Partial re-runs — only what changed
- Multi-select copy and paste, notes, branch colours and names
- Analysis Wizard and node suggestions
Workflow templates
33 templates across 5 modalities, with sample data.
- Open, run, then edit any node
- 10 templates wait at a Resource Center node until it is installed
- Branch a template into your own pipeline
Resource Center
External databases and models are installed before a run, never during one.
- Pinned versions, SHA-256, licence acceptance
- CellPhoneDB, CellTypist, OmniPath, JASPAR, PROGENy, Hallmark, CollecTRI, cCRE
- Methylation manifests and annotation
Memory guard
Peak memory is predicted per node before it runs.
- Admits or refuses with a message naming what holds memory
- Re-measures near-misses instead of refusing on a snapshot
- Watchdog and diagnostics export
Projects
Save, open, export and import as a single .bioflow file.
- Cached results reopen without re-running
- Export bundles receipts and an RO-Crate
- Save H5AD and Export CSV nodes for downstream tools
Install and sign in
One installer for Windows 10/11; sign in at every launch.
- Bundled Python engine — no conda, no R
- One active device per account
- Auto-update and a log panel
Built for the bench, not the cloud.
A desktop app with its own engine
Electron front end, a bundled Python engine behind it on localhost. Your counts, IDATs and Xenium folders are read from disk and stay on disk. Windows 10/11, 64-bit.
The libraries you would cite anyway
Scanpy, Squidpy, PyDESeq2, scvelo, CellRank, decoupler, LIANA, CellPhoneDB, CellTypist, harmonypy, Scrublet, gseapy, Hotspot, mepylome and pyJASPAR, called through nodes instead of a notebook. BANKSY spatial domains and cellular neighborhoods are native implementations.
A graph executor, not a script runner
Nodes form a DAG. Change a parameter and only the downstream nodes are invalidated and re-run; cached results reopen from a saved project; a running node can be cancelled. Large results live outside the node card so the canvas stays light.
Local compute, online sign-in
Every node runs on your machine. The app verifies your account at launch, so it needs a connection to start, and the optional AI Copilot sends node names, parameters and small summaries only. External resources download once, from the Resource Center, before a run.
Counts are read from the node catalog that the app generates — 892 parameters in total, documented per node under Docs → Nodes.
September 2026: Oreumics, and a quieter memory guard.
- 01
BioFlow Copilot is now Oreumics
Same app, same local-first design, a new name and mark. Projects, .bioflow files, sign-in and access tickets carry over unchanged.
- 02
Connect an AI assistant, in-app
A guided dialog replaces the separate window. Claude Desktop gets a Save extension file… step (the Microsoft Store edition cannot open .mcpb by double-click); the Codex app and Claude Code have their config written for them; the dialog confirms the first real request.
- 03
Runs that fit in memory are admitted
Nodes are charged only for the matrices they read, the disk cache quota is a cleanup target instead of a wall, dense matrices are converted to sparse on load, and Normalize and Log1p share buffers.
- 04
Resource Center follow-ups
A missing database stops the node with a message naming the resource, CellPhoneDB databases installed through the Resource Center are recognised, and the AI can ask which resources are installed before proposing a plan.
- 05
Spatial viewer and canvas fixes
Polygon selection, per-group highlighting and a zoom that survives re-rendering; large tables no longer cut off mid-stream. Multi-select Ctrl+C works again and Merge Cell Meta resolves auto-match the same way in preview and run.
- 06
Reproducible Draw Graph and a modality-first library
Force-directed layouts are seeded and report the layout actually used. The Node Library is organised by modality first.
See it in action.
Free during the beta — access by admin-issued ticket. No credit card required.