DataDownload.txt

The steps below are for HPAP data downloading.
1. Install Python 3.7 or above (https://www.python.org/downloads/)
2. Install Python packages
     - Pandas https://pandas.pydata.org/pandas-docs/stable/getting_started/install.html
     - Blackfynn client https://developer.blackfynn.io/python/latest/quickstart.html#installation
         * After blackfynn installation, please set the "bf_profile"
         * API token: [To Be Set]
         * API secret: [To Be Set]
3. Download data
     - Command: python bfsync.py [options, or -h for help]
     - Data categories: "Clinical data", "B cell receptor repertoire", "Flow panels for B cells", "Flow cytometry - Immune lineage", "Histology", "CyTOF", "ATACseq", "mRNAseq", "Sequencing data for sorted cells/Sort data", "WGBS", "Single-cell RNAseq", "Calcium imaging", "Patch-Clamp", "Oxygen consumption", "Morphology and viability", "Perifusions", "Imaging mass cytometry", "ATAQseq", "Tetramer Ag specific studies by FACS".
     - For example, to download scRNAseq data for donor HPAP-008, the command is:
     
         python bfsync.py -d "HPAP-008" -c "Single-cell RNAseq"