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Shanghua
61 lines
2.7 KiB
ReStructuredText
61 lines
2.7 KiB
ReStructuredText
Transcriptformer Tools
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======================
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**Configuration File**: ``remote_tools/transcriptformer_tools.json``
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**Tool Type**: Remote
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**Tools Count**: 1
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This page contains all tools defined in the ``transcriptformer_tools.json`` configuration file.
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Available Tools
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---------------
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**run_transcriptformer_embedding_retrieval** (Type: RemoteTool)
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Retrieves contextualized gene embeddings from Transcriptformer models. This tool provides access ...
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.. dropdown:: run_transcriptformer_embedding_retrieval tool specification
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**Tool Information:**
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* **Name**: ``run_transcriptformer_embedding_retrieval``
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* **Type**: ``RemoteTool``
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* **Description**: Retrieves contextualized gene embeddings from Transcriptformer models. This tool provides access to pre-computed Transcriptformer embeddings that capture gene expression patterns learned from single-cell RNA sequencing data. The embeddings are contextualized for specific combinations of disease states and cell types, enabling precise analysis of gene behavior in relevant biological contexts.
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**Parameters:**
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* ``state`` (string) (required)
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Disease state context for embedding retrieval. Examples: 'control': Healthy/normal condition; 'disease': Disease-affected state; 'treated': Post-treatment condition; 'untreated': Pre-treatment condition. Must match available states in the disease-specific store.
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* ``cell_type`` (string) (required)
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Cell type context for embeddings. Examples: 'b_cell': B lymphocytes; 't_cell': T lymphocytes; 'macrophage': Tissue macrophages; 'epithelial_cell': Epithelial cells; 'fibroblast': Connective tissue fibroblasts. Must match available cell types in the disease store.
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* ``gene_names`` (array) (required)
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Gene identifiers for embedding retrieval: Gene symbols: ['TP53', 'BRCA1', 'EGFR', 'MYC']; Ensembl IDs: ['ENSG00000141510', 'ENSG00000139618']; Mixed formats supported; Empty list retrieves all available genes.
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* ``disease`` (string) (required)
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Disease/dataset identifier. Examples: 'breast_cancer': Breast cancer scRNA-seq data; 'lung_cancer': Lung cancer contexts; 'diabetes': Diabetes-related datasets; 'alzheimer': Alzheimer's disease contexts. Must match available disease stores.
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**Example Usage:**
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.. code-block:: python
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query = {
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"name": "run_transcriptformer_embedding_retrieval",
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"arguments": {
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"state": "example_value",
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"cell_type": "example_value",
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"gene_names": ["item1", "item2"],
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"disease": "example_value"
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}
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}
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result = tu.run(query)
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Navigation
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----------
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* :doc:`tools_config_index` - Back to Tools Overview
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* :doc:`remote_tools` - Remote Tools Setup
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