Singler Tools

Configuration File: remote_tools/singler_tools.json Tool Type: Remote Tools Count: 1

This page contains all tools defined in the singler_tools.json configuration file.

Available Tools

run_singler_annotate (Type: RemoteTool)

Annotate single cells with SingleR (Aran 2019): correlate each cell against a labeled reference t…

run_singler_annotate tool specification

Tool Information:

  • Name: run_singler_annotate

  • Type: RemoteTool

  • Description: Annotate single cells with SingleR (Aran 2019): correlate each cell against a labeled reference transcriptome and assign the best-matching cell-type label, per cell (not per cluster) — the standard reference-based alternative to manual marker annotation. Reference is either a built-in celldex panel (HumanPrimaryCellAtlasData, BlueprintEncodeData, MonacoImmuneData, …) or your own labeled .h5ad (ref_adata_path + ref_labels_key). Returns a label for every cell plus label counts. Input is a server-accessible query .h5ad of log-normalized expression.

Parameters:

  • adata_path (string) (required) Server-accessible path to the query .h5ad (log-normalized expression in .X).

  • celldex_ref (string) (optional) Built-in reference name: HumanPrimaryCellAtlasData, BlueprintEncodeData, MonacoImmuneData, DatabaseImmuneCellExpressionData, NovershternHematopoieticData, ImmGenData, or MouseRNAseqData. Omit when using a bring-your-own reference.

  • ref_label_field (string) (optional) celldex label granularity: ‘label.main’ (default) or ‘label.fine’.

  • ref_adata_path (string) (optional) Bring-your-own reference .h5ad (log-normalized); used when celldex_ref is omitted.

  • ref_labels_key (string) (optional) obs column in ref_adata_path holding the reference cell-type labels.

Example Usage:

query = {
    "name": "run_singler_annotate",
    "arguments": {
        "adata_path": "example_value"
    }
}
result = tu.run(query)