Query genomic datasets via labretriever VirtualDB views in DuckDB.
npx skills add https://github.com/cmatKhan/labretriever --skill vdb
Please help me install this Agent Skill. Skill: vdb Source: https://github.com/cmatKhan/labretriever/tree/main/skills/vdb Command: npx skills add https://github.com/cmatKhan/labretriever --skill vdb
labretriever's VirtualDB provides a unified SQL interface over genomic and transcriptomic datasets hosted on HuggingFace, enabling researchers to query, explore, and compare datasets without manual data wrangling.
Connect to the MCP server and run a sample query using vdb.query.
High-intent search queries and answers about installing and using this skill.
You can query genomic datasets hosted on HuggingFace using SQL by leveraging VirtualDB views in DuckDB. This provides a unified SQL interface over heterogeneous genomic resources, enabling you to execute queries without manual data wrangling.
To discover transcriptomic datasets and inspect their schemas, use list_datasets to find available resources and describe_dataset to inspect schemas. You can also retrieve semantic metadata using get_column_metadata and provenance tags via get_tags.
Yes, you need a connected labretriever MCP server and a valid VirtualDB config to query genomic data with DuckDB. These prerequisites allow you to access the '{name}' and '{name}_meta' views and execute SQL queries using the vdb.query helper tool.
Yes, VirtualDB provides a unified SQL interface over HuggingFace-hosted datasets, letting you explore and compare schemas directly. You can use describe_dataset and describe_dataset_meta to inspect structures and retrieve metadata without downloading entire datasets.
You execute SQL queries across HuggingFace resources using vdb.query against the '{name}' and '{name}_meta' views in DuckDB. The Skill also supports reproducing MCP results in Python when needed for downstream analysis or validation.
cmatKhanInspect and audit HuggingFace dataset repositories via the labretriever DataCard API.
bettercallfanAnalyze Excel and CSV files with SQL queries via DuckDB.
Imad-OuteManage and analyze BAM, CRAM, VCF, BCF, FASTA, and FASTQ genomic files.
ragnarokhaaFetch and integrate bioinformatics skills and resources for genomic and transcriptomic analyses.
