Tutorials & Notebooks

The notebooks are ordered as a learning path. Start with the Python API, then move through command-line usage, download planning, search, publication identifiers, optional metadata enrichment, and BioScience search parsing.

The download notebooks intentionally preview commands and selected rows rather than fetching large sequencing files during documentation builds.

Tutorials

• pysradb notebooks
• Python API Demo
• Command-line Download
• Parallel Download
• Converting SRA to FASTQ using Conda
• Selecting Subsets of a Project
• Querying Multiple Projects
• Query and Search
• Extract Identifiers from PMC/DOI
• Metadata Enrichment with Optional LLM Backends
• Parse BioScience Search

You can also view the complete notebooks directory on GitHub for additional tutorials and examples.

Potential Future Vignettes

The current notebooks cover the main Python API, command-line downloads, parallel download planning, subset selection, multi-project metadata, search, publication identifiers, metadata enrichment, and BioScience search parsing. Useful follow-up vignettes would be:

• an accession conversion cookbook for GSE, GSM, SRP, SRX, SRS, and SRR mappings;

• GEO matrix download and parsing workflows;

• detailed sample-attribute expansion with --desc and --expand;

• search summaries that use --stats and --graphs.