CyteArc keeps the familiar biological sequence of quality control, feature selection,
normalization, reduction, neighbourhood graphs, embeddings, clustering, and marker discovery.
The main change is how the work is executed. A CyteArc DataStore opens a Zarr store on local disk
or object storage, streams bounded blocks, and writes each completed result back as an immutable
artifact.
Choose the guide for the ecosystem you already use:
CyteArc for Scanpy users maps Scanpy stages and explains H5AD transfer.
CyteArc for Seurat users maps Seurat stages, RDS import, and multimodal WNN analysis.
If you want to run CyteArc before comparing APIs, start with the Quick start.
Where CyteArc fits¶
CyteArc is most useful when:
the count matrix is too large for convenient in-memory analysis
counts should stay on local disk or object storage while the analysis runs
completed steps should persist so they can be inspected or reused
RNA, ATAC, or CITE-seq assays should live in one analysis store
You do not need to move an entire project to CyteArc. A common pattern is to run the large, graph-based part of an analysis in CyteArc, then export the required data for a method in another single-cell ecosystem. CyteArc does not include scVI, Scanorama, RNA velocity, or replicate-aware differential expression.
The mental-model change¶
| Familiar concept | CyteArc |
|---|---|
An AnnData or SeuratObject holds counts, metadata, and results | A DataStore opens a Zarr store containing counts, metadata, and results |
| Analysis changes an object in the current session | Each supported analysis step persists an immutable artifact |
| Filtering subsets an object or creates a view | Filtering returns an immutable selection artifact without deleting cells |
| Graphs and embeddings occupy named object slots | Graphs and embeddings are passed by exact artifact reference |
| One object exposes an active result set | A PipelineRun exposes one durable frozen result set without replacing other runs |
Feature selection is artifact-only. A call such as features = ds.features.hvgs(cells, ...) returns
an immutable reference that normalization and downstream methods consume. Related analysis
branches can therefore coexist in one datastore without an implicit active result replacing an
earlier one.
See Why CyteArc records provenance for the result model and Import and export for the full format contracts.