Data
The Data section prepares everything downstream analysis needs.
Datasets
Upload or convert data files:
| Format | Notes |
|---|---|
.h5ad | Preferred; validated at ingest |
| CSV/TSV count matrix | Converted to AnnData with Import |
10x HDF5 (.h5) | Converted with Import |
| 10x MTX zip bundle | Converted with Import (optional cell_metadata.csv and embedding_<name>.csv are carried in) |
Seurat / SingleCellExperiment .rds, .rda, .RData | Converted with Import, read in Python without R; metadata, reductions, and identities are kept |
See File formats for details.
After upload, the dataset row shows cell/spot counts, gene count, ingestion status, and compact Bioconductor compatibility badges when AnnData layers or obsm entries map to counts, logcounts, scaled data, protein, or spatial coordinates. Failed ingestions display an error message you can use to fix the file.
Dataset attachments
Two optional files can be attached under a ready dataset:
| Attachment | File | Used by |
|---|---|---|
| Raw droplet matrix | Cell Ranger raw_feature_bc_matrix.h5, or the folder as a zip | SoupX-style ambient RNA correction |
| Velocity counts | velocyto .loom, or an .h5ad with spliced and unspliced layers | RNA velocity, and the spliced fraction in Preparation Method Comparison |
Each shows its file name and size with Replace and Remove. Cells in velocity counts are matched to the dataset by barcode.
Metadata
Define a metadata table keyed to barcodes or sample IDs in the dataset. Columns typically include sample, condition, donor, and batch. Before each analysis run the platform validates that join keys match and merges columns into AnnData obs.
Use Validate against dataset to catch mismatched IDs before running expensive jobs.
Design
Specify which obs columns define biological groups and which column identifies biological replicates. The design table feeds contrast definitions and future bulk statistical models.
Contrasts
Save named comparisons (for example Treatment vs Control on the condition column). Contrasts appear in the Analyze DE step when comparison mode is condition or sample.
Ingestion
The Ingestion panel summarizes format detection, conversion jobs, and any sidecar files used during CSV/10x/R-object import. Uploading a dataset marks the study's earlier runs out of date.
Tips
- Run metadata validation after every metadata edit; stale flags appear on History if you change metadata after DE.
- Spatial datasets must include
obsm['spatial']coordinates in the.h5ad. - Biomarker workflows need a label column with at least two classes (default:
conditioninobs).