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File Formats of the Data Processing Pipelines Service

DCP Matrix Download File Format

MTX and CSV Matrix Deprecation Notice: DCP 1.0 matrices will be deprecated in the DCP 2.0. Loom files will be the default format.

Cell by gene count matrices are provided in Loom file format and be downloaded through the HCA Data Portal. From the Portal's Data Browser, you can make a multifaceted search to download matrices for multiple projects. Alternatively, you can explore the matrices available for download on the individual Project pages.

Working with Loom Files

Loom files can be explored using multiple Python- and R-supported downstream analysis tools, including Loompy, SCANPY, and Pegasus. You can also visualize Loom files using Bioconductor's LoomExperiment.

Contributor-generated Matrix File Format

When available, contributor-generated count matrices will be provided on individual Project pages. These matrices will vary in file format and content. To learn more about a specific contributor-generated matrix file, reach out to the Contacts listed on the Project page.

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