About Scvi Tools MCP
Scvi Tools MCP is an MCP server published by YosefLab in the Security category: mCP (Model Context Protocol) server for deep probabilistic analysis of single-cell omics data using scvi-tools.
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Install
git clone https://github.com/YosefLab/scvi-tools-mcpThis server has no ConduID identity, so agent calls to it are not receipted. Pin the version you install and review the source before granting it credentials.
Tools (25)
get_api_referenceSignature + docstring for any public class or function
Parameters not published.
get_downstream_guideGuide for DE, clustering, embedding, label transfer
Parameters not published.
get_faqCurated FAQ from docs, GitHub issues, and Discourse
Parameters not published.
get_hub_modelInspect one pretrained HubModel repo
Parameters not published.
get_model_overviewFull model description, use cases, inputs, outputs
Parameters not published.
get_model_parametersKey `__init__` and `train()` parameters with defaults
Parameters not published.
get_scib_metricAPI reference for one scib-metrics metric or benchmark
Parameters not published.
get_scib_metrics_tutorialPaginated scib-metrics tutorial content
Parameters not published.
get_scviva_modelAPI reference + user guide for one scviva-tools model
Parameters not published.
get_scviva_tutorialPaginated scviva-tools tutorial content
Parameters not published.
Show all 25 tools
get_setup_anndata_guideExact `setup_anndata()` call + required obs/var fields
Parameters not published.
get_tutorialPaginated tutorial content (code + prose, no outputs)
Parameters not published.
get_workflow_templateStep-by-step code template for an analysis task
Parameters not published.
list_hub_modelsBrowse official scvi-tools Hugging Face Hub models
Parameters not published.
list_scib_metricsBrowse scib-metrics integration-benchmarking metrics
Parameters not published.
list_scib_metrics_tutorialsBrowse scib-metrics tutorials
Parameters not published.
list_scviva_modelsBrowse scviva-tools spatial models (ResolVI, DestVI, …)
Parameters not published.
list_scviva_tutorialsBrowse scviva-tools tutorials
Parameters not published.
list_tutorialsBrowse tutorials by category
Parameters not published.
recommend_modelRank models by task and data type — start here
Parameters not published.
search_apiSearch public symbols by keyword
Parameters not published.
search_knowledgeCross-search all knowledge (catch-all)
Parameters not published.
search_tutorialsKeyword search across all tutorials
Parameters not published.
suggest_hub_modelsSuggest Hub models for reference/query workflows
Parameters not published.
validate_data_requirementsPass/fail checklist for your AnnData against a model
Parameters not published.
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