The manual.
Everything about the Oreumics desktop app — from the first install to a figure you can submit, and a Methods paragraph to go with it.
119
nodes
14
categories
22
loaders
93
plot types
33
templates
5
modalities
Getting started
Working in the app
The canvas is where analysis happens; the workspaces are where figures and thresholds are tuned without re-running anything.
Canvas, tabs & branches
Workflow tabs, split panes, running only what changed, notes, branch labels, copy and paste.
Templates & Analysis Wizard
33 ready-made workflows plus a three-step wizard; 10 templates need a resource installed first.
Visualization Workspace
Five shared sections, per-group colours, group renaming, legend placement, export.
Figure Canvas
Assemble finished figures freely with annotations, crop and export.
Product page
Resource Center
Databases, priors and models a node needs — installed once, pinned, never fetched mid-run.
Memory & large data
How a run is admitted or refused, and what to change when it is.
Saving, citing & provenance
.bioflow projects, run receipts, RO-Crate, the Methods paragraph, exports.
AI
Two ways to put a language model to work: the in-app AI Copilot, or an assistant you already use (Claude Desktop, the ChatGPT desktop app, Claude Code) connected over MCP. Both act on the visible canvas.
AI Copilot
Bring your own API key; ask about results; Apply / Undo action plans; Approve & Run; reports.
Connect an AI assistant
Claude Desktop via the extension file, ChatGPT desktop app (Codex) and Claude Code via auto-written config.
Automated reports
Outline detected from the graph, an emphasis step, then HTML or PDF.
Product page
Tutorials
Step-by-step walkthroughs, one per analysis type.
PBMC scRNA-seq
QC → clustering → markers on the classic 3k dataset.
Multi-sample integration
Merge samples and keep track of where each cell came from.
Harmony integration
Batch correction on the PCA space, then a shared embedding.
Trajectory (PAGA + DPT)
Topology and pseudotime along a differentiation path.
RNA Velocity
Spliced / unspliced dynamics with scvelo.
Visium spatial
Neighborhoods, co-occurrence and autocorrelation on a tissue section.
Xenium spatial
Single-cell resolution imaging data, from density QC to statistics.
Bulk RNA-seq
Counts to DESeq2 differential expression and pathways.
DNA methylation
IDAT or beta matrix to DMPs, DMRs and enrichment.
ATAC-seq
Peaks, LSI, clustering and motif enrichment.
Pathway & interaction
Enrichment and cell–cell communication after DEG.
Node reference
Every node with its parameters, defaults and plot types — generated from the app so it cannot drift. 119 nodes across 14 categories, or browse the way the app's Node Library does: by modality, in pipeline order.
All nodes (119)
Search by name, filter by category or modality.
By modality (5)
The Node Library’s staged views, loader to plot.
scRNA-seq
66 nodes · 8 loaders · 20 templates
Spatial
50 nodes · 10 loaders · 4 templates
Bulk RNA-seq
19 nodes · 4 loaders · 3 templates
Methylation
19 nodes · 3 loaders · 4 templates
ATAC-seq
17 nodes · 4 loaders · 2 templates
Input / Output
16Loaders, merging, subsetting, save/export.
Preprocessing
6QC, normalize, log1p, HVG, scale, doublet detection.
Analysis
8PCA, neighbors, UMAP, t-SNE, clustering, DEG, Harmony.
Trajectory
8PAGA, DPT, diffusion map, draw graph, RNA velocity.
CellRank
5Markov-chain fate analysis: kernel, fate, drivers, gene trends.
Annotation
4LLM-based and reference-based cell type annotation.
Pathway
2Top-DEG list extraction and Enrichr GO/KEGG enrichment.
Functional Activity
3Expression-based pathway and transcription-factor activity inference.
Cell-Cell Communication
4Ligand-receptor interaction analysis — CellPhoneDB + LIANA consensus.
Visualization
9Embeddings, markers, HVG, doublet, trajectory, velocity, pathway plots.
Spatial
24Spatial coordinates, density QC, grouping, neighbors, squidpy stats.
Bulk RNA-seq
9featureCounts/Salmon/Kallisto loaders, DESeq2 DE, GSEA.
Methylation
12IDAT/beta loaders, DMP/DMR, directional GOmeth, cCRE/BED enrichment.
ATAC-seq
9Fragments/peak loaders, LSI, motif analysis.