Skill Claude CodeCodex
Diagnose a failing Nextflow pipeline run in an OpenProblems benchmark. Use when a nextflow run fails, a process errors out, or the user shares a .nextflow.log / .command.err and asks why it broke.
Skill Claude CodeCodex
Prepare a spatial transcriptomics method for contribution to an OpenProblems benchmark (e.g. taskistpreprocessing). Use when the user wants to submit/contribute a method, open a PR to a task repo, or check submission readiness.
Skill Claude CodeCodex
Validate and inspect spatial transcriptomics data files (SpatialData/zarr/AnnData) before any analysis. Use when the user points at a spatial data file, reports a loading/format error, or asks whether data is suitable for a method.
Skill Claude CodeCodex
Author or modify a Viash component (config.vsh.yaml + script) for an OpenProblems method, especially a taskistpreprocessing stage. Use when the user wants to add/implement a spatial method, scaffold a component, or fix a config.vsh.yaml.
Plugin Claude Code
Plugin marketplace listing 1 plugin: openproblems-spatial.
Plugin Claude Code
Domain skills + MCP validation tools for OpenProblems spatial transcriptomics benchmarks (SpatialData/zarr, Viash, the iST preprocessing pipeline).
Cursor rule Cursor
Diagnose a failing Nextflow pipeline run in an OpenProblems benchmark. Use when a nextflow run fails, a process errors out, or the user shares a .nextflow.log / .command.err and asks why it broke.
Cursor rule Cursor
Prepare a spatial transcriptomics method for contribution to an OpenProblems benchmark (e.g. taskistpreprocessing). Use when the user wants to submit/contribute a method, open a PR to a task repo, or check submission readiness.
Cursor rule Cursor
OpenProblems spatial transcriptomics co-pilot — project rules.
Cursor rule Cursor
Validate and inspect spatial transcriptomics data files (SpatialData/zarr/AnnData) before any analysis. Use when the user points at a spatial data file, reports a loading/format error, or asks whether data is suitable for a method.
Cursor rule Cursor
Author or modify a Viash component (config.vsh.yaml + script) for an OpenProblems method, especially a taskistpreprocessing stage. Use when the user wants to add/implement a spatial method, scaffold a component, or fix a config.vsh.yaml.
Instructions file GitHub Copilot
Instructions for Rebell-Leader/SpatialAI_MCP, covering agents.md — openproblems spatial transcriptomics co-pilot, what this project is, ground truth: which mcp tools actually exist, domain rules (spatial transcriptomics) and coding standards.
MCP server Claude CodeCodexCursor +2
MCP server "openproblems-spatial" as configured in Rebell-Leader/SpatialAIMCP. Launched with openproblems-mcp-server. Needs 1 environment variable to run.
Instructions file CodexOpenCode
Instructions for Rebell-Leader/SpatialAI_MCP, covering agents.md — openproblems spatial transcriptomics co-pilot, what this project is, ground truth: which mcp tools actually exist, domain rules (spatial transcriptomics) and coding standards.
Instructions file
Instructions for Rebell-Leader/SpatialAI_MCP, covering claude.md and claude code notes.
Instructions file Gemini CLI
Instructions for Rebell-Leader/SpatialAI_MCP, covering agents.md — openproblems spatial transcriptomics co-pilot, what this project is, ground truth: which mcp tools actually exist, domain rules (spatial transcriptomics) and coding standards.