Sage-Bionetworks

Sage-Bionetworks/agent-skills

Plugin Claude Code

Agent skills for Sage Bionetworks — data science, bioinformatics, and research tooling.

Sage-Bionetworks/agent-skills

Plugin Claude Code

A collection of agent skills for Sage Bionetworks — data science, bioinformatics, and research tooling.

Sage-Bionetworks/agent-skills

Agent

Audits an existing CLAUDE.md for accuracy — scores it against the rubric and confirms which references are stale. Returns baseline score + confirmed accuracy issues.

Sage-Bionetworks/agent-skills

Agent

Analyzes code & data-model changes in a scope since a commit for CLAUDE.md evolution. Returns a distilled change digest, never raw diffs.

Sage-Bionetworks/agent-skills

Agent

Scouts directories lacking a CLAUDE.md for convention density and decides own-file vs roll-up vs already-covered. Reads source deeply internally; returns coverage decisions only.

Sage-Bionetworks/agent-skills

Agent

Mines GitHub PRs & issues for conventions and anti-patterns to feed CLAUDE.md evolution. Reads verbose PR/review threads internally; returns a short evidence-backed candidate list.

Sage-Bionetworks/agent-skills

Agent

Mines Jira tickets/epics and Confluence pages for constraints to add or lift in CLAUDE.md. Reads full pages internally; returns a short list keyed by ticket/page.

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

Brief description of what this skill enables Claude to do and what tool/service it covers.

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

Create initial CLAUDE.md files for a repo with none — auto-detects stack, pulls context from GitHub/Jira/Confluence, produces concise files focused on non-obvious patterns.

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

Update existing CLAUDE.md files by analyzing code changes, GitHub PRs/issues, Jira/Confluence since last modification, with full accuracy audit.

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

Query the NIH RePORTER API (api.reporter.nih.gov) for federally-funded research projects and publications. Covers POST /v2/projects/search and POST /v2/publications/search — criteria payload construction, pagination, rate-limit handling, and the criteria→response field-name mapping that trips up most callers.

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

Patterns for extracting and normalizing metadata from scientific data repositories (GEO, SRA/ENA, PRIDE, BioStudies, PubMed) and publication sources. Covers per-sample identifier derivation, author name normalization, assay type determination, species verification, file format normalization, and a 4-tier gap-fill…

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

Advanced patterns for curating data in Synapse (synapse.org) via the REST API. Covers the annotations2 endpoint with etag/optimistic-locking, Dataset entity creation with dynamically-derived column schemas, JSON Schema binding for metadata validation, team permissions, and wiki management. Complements the…

Sage-Bionetworks/agent-skills

Skill Claude CodeCodex

The Synapse Python client (synapseclient) is the official Python SDK and CLI for Synapse (synapse.org), a collaborative biomedical data sharing platform by Sage Bionetworks. The modern synapseclient.models API provides async-first dataclass models with auto-generated sync wrappers.

Sage-Bionetworks/synapse-mcp

Instructions file

Instructions for Sage-Bionetworks/synapse-mcp, covering project, stack, commands, tool authoring and bm25 discovery transform.

Sage-Bionetworks/synapse-mcp

MCP server Claude CodeCodexCursor +2

Sage Bionetworks' Synapse server: lets the agent find and read datasets, files and projects on the Synapse research data platform. Remote server at mcp.synapse.org.