Downloads and exports

You can download the data behind your results in standard formats, ready for analysis in Python, R, or a spreadsheet.

What you can download

Export	Format	Contents
Expression table (Compact)	.tsv	Expression values for the visible cell types and samples, respecting the active filters
Expression table (Full)	.zip	All cell types, all samples, and every metadata column, unfiltered
Per-cell expression matrix	.zip	Sparse cell-by-feature matrix of your query genes, plus cell IDs and barcodes
All cells	.tsv.gz	Sample, cell ID, cell type, and total counts for the selected samples
Coverage matrix	.tsv	Coverage data for the matched samples in the Coverage Explorer

Bulk exports are limited to 50 samples per download.

Download a per-cell expression matrix

1. Run a search in the Expression Explorer.
2. Click Download and choose Per-cell expression matrix.
3. In the export modal, select the samples you want to include.
4. Click Queue positive-cell ZIP. The browser downloads a ZIP archive containing the sparse matrix file, a manifest that describes each file and its columns, and the cell IDs and barcodes.

The same modal offers Selected all cells, which downloads the sample and cell table for the selected samples as a gzipped TSV. Use it when you need the full cell universe for a set of samples, for example as the denominator for downstream calculations.

Download an expression table

1. Open the result of a search.
2. Click Download and choose Compact for a filtered TSV of the currently visible cell types and samples, or Full for an unfiltered ZIP with all cell types, all samples, and all metadata columns.

Download coverage

1. Run a search in the Coverage Explorer.
2. Click Download and choose Coverage matrix to save the coverage values for the matched samples.