ebi-ait/hca-matrix-downloader

Python client for the DCP matrix service (prototype)

Human Cell Atlas Matrix Service Client

This small cli enables the retrieval of data from the Human Cell Atlas Matrix Service for a particular experiment in either Loom or Matrix market format.

1. Go to the HCA Data Browser: https://prod.data.humancellatlas.org/explore/projects
2. Under "Search", write in "matrix". This will limit the projects to those supporting the matrix formatting
3. Click on a project of interest in the list, e.g. this one: https://prod.data.humancellatlas.org/explore/projects/cddab57b-6868-4be4-806f-395ed9dd635a
4. Call the downloader, providing either one of the project names (Project Title, Project Label or the ID from the link) or a Matrix API query in JSON. Any of these arguments would work:

-p "Single cell transcriptome analysis of human pancreas"
-p "Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns."
-p cddab57b-6868-4be4-806f-395ed9dd635a
-q '{"filter": {"field": "project.project_core.project_short_name", "value": "Single cell transcriptome analysis of human pancreas", "op": "="}}'

For complete usage information, use -h.

A shell script for converting HCA mtx to 10X(v2)-compatible mtx is provided.