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.
- Go to the HCA Data Browser: https://prod.data.humancellatlas.org/explore/projects
- Under "Search", write in "matrix". This will limit the projects to those supporting the matrix formatting
- 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
- 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.