scExplorer

Step 0 · dataset intake

Upload your data

Analysis name pending Human · Symbol Files pending Not ready

Analysis Name:

Stored with the UUID and reused in Results, My Analyses and comparisons.

Species:

Used for mitochondrial gene parsing and species-aware downstream resources.

Gene ID:

Must match `var_names`: symbols such as CD3D, or Ensembl IDs.

Email:

Optional notification target after upload finishes.

Drop an `.h5ad`, `.h5`, `.rds`, or complete 10x MTX bundle here.

No files selected.

File readiness No dataset selected

Choose one single-cell object or the complete 10x MTX triplet before uploading.

Format Pending Files 0 Total size 0 B

Format & Size Requirements

.h5ad (AnnData): Version 0.8+ recommended; cells in obs_names, genes in var_names. Gene IDs should match the selected Species and Gene ID.
.h5 (10x HDF5): Cell Ranger HDF5 (v2/v3) is supported; converted server‑side to .h5ad.
.rds (Seurat): Seurat object is converted server‑side to .h5ad via zellkonverter.
10x MTX bundle: Upload together in the same selection: matrix.mtx or matrix.mtx.gz, barcodes.tsv or barcodes.tsv.gz, and genes.tsv or features.tsv (optionally .gz). Do not ZIP; upload the files directly.
Compression: .gz supported for 10x TSV/matrix files. ZIP archives are not processed automatically.
Limits: Max 2 GB per file; up to 3 files per upload.

Chrome Connector (Beta)

Import datasets directly from GEO, EMBL-EBI Single Cell Expression Atlas, CELLxGENE Discover, Human Cell Atlas, and Broad Single Cell Portal.

Download the ZIP file and extract it locally.
Open chrome://extensions in Google Chrome.
Enable Developer mode and click Load unpacked.
Select the extracted scexplorer-connector folder.
Open the connector popup and set scExplorer URL to the site root, for example https://apps.cienciavida.org.
Visit a supported portal dataset page. The connector panel will detect compatible files and send them directly to scExplorer.

This connector is currently in beta. It is suitable for guided import workflows, but portal-specific layouts and file conventions may still evolve.