CxG / Tier 1 to DCP spreadsheet

This is a project to convert the Human Cell Atlas Tier 1 metadata fields from a published CELLxGENE dataset, to the 'HCA DCP metadata schema' based, ingestible spreadsheet.

Usage

To convert there are two notebooks

• cellxgene_metadata_export.ipynb to download using the CELLxGENE API and export to a csv file
• dcp_metadata_import.ipynb to create a list of dataframes (based on the mapping of fields specified on tier1_to_dcp_dict.py) and export as an excel spreadsheet with the HCA style.

Please specify the collection_id and the dataset_id in the corresponding fields both notebooks. Everything else should be automated.

Requirements

The packages needed for these notebooks are listed in the requirements.txt file. To install via pip use:

pip install -r requirements.txt

Known limitations

Sequence file tab is filled only with run ID & library ID (since we don't have file_names of fastq files)

TODO