In Claude (claude.ai, and Claude's desktop and phone apps), baSeq can be a connector: ask Claude about your datasets, analyses and findings, and it looks them up on baSeq as you. It reads only: it cannot add, change or delete anything.

Connect it

1. In Claude, open Settings, then Connectors, and add a custom connector named baSeq with the address https://baseq.bio/mcp.
2. Choose Connect. baSeq asks you to sign in, then shows what Claude asks for.
3. Type your password and a two-step code, as when you make an API key, and choose Allow.

You need two-step sign-in on (your Account page). In a Claude Team or Enterprise plan, the plan's owner may need to add the connector first; each person then connects it with their own baSeq account.

Ask

For example: “Which of my datasets have dexamethasone?”, “What have we found about ZBTB16?”, “Show the significant genes of my Airway analysis” or “Give these Ensembl ids their gene names”. Claude can find datasets by words, organism and sample sheet columns, read a dataset's sample sheet and versions, find analyses and read their steps, findings and the first rows of their tables, list an analysis's significant genes, search what your analyses found, gather everything about one gene, as the gene card does, and name genes from baSeq's gene reference. It links to the pages on baSeq.

In Claude Code

claude mcp add --transport http baseq https://baseq.bio/mcp

Then type /mcp in Claude Code and connect baSeq as above. For code that reads and adds data, use baseqdb (From Python and R).

What leaves baSeq

Data you fetch with a key leaves baSeq, and so does what Claude reads. Our Data Processing Agreement does not cover what an AI agent or another service then does with it. Claude reads what each question needs, such as the first rows of a table rather than the whole file.

End it

The connection is listed with your API keys on your Account page, as Claude (claude.ai). It ends after 90 days; Revoke ends it sooner, and so do turning two-step sign-in off and a new password.