SingleR Remote Tool (MCP Server)

Serves SingleR (Aran et al., Nature Immunology 2019) — reference-based single-cell annotation — as the ToolUniverse remote tool run_singler_annotate.

SingleR labels each cell (not each cluster) by correlating its expression against a labeled reference transcriptome and assigning the best-matching cell type. It is the standard automated alternative to manual marker-gene annotation.

Served remotely because the engine is R/Bioconductor (SingleR + celldex). The Python side reads the query .h5ad with scanpy and hands the matrix to the bundled singler_annotate.R over a MatrixMarket interchange — no zellkonverter/basilisk required (the heavy R↔Python bridge is avoided).

Two reference modes:

• built-in — a celldex panel by name (HumanPrimaryCellAtlasData, BlueprintEncodeData, MonacoImmuneData, DatabaseImmuneCellExpressionData, NovershternHematopoieticData, ImmGenData, MouseRNAseqData), downloaded on the server.

• bring-your-own — a labeled reference .h5ad (ref_adata_path + ref_labels_key).

Supply log-normalized expression for both query and reference (SingleR’s default assumption).

Deploy

pip install -r requirements.txt            # scanpy + scipy (Python side)
Rscript -e 'BiocManager::install(c("SingleR","celldex","jsonlite"))'   # R side
python singler_tool.py                      # starts the MCP server on 127.0.0.1:8029

Rscript must be on PATH (or set RSCRIPT_BIN). Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse

Tool definition: src/tooluniverse/data/remote_tools/singler_tools.json (type: RemoteTool).