get_initial_predictions

This function retrieves initial cell type predictions from all specified models.
It is an internal helper function used by the interactive_consensus_annotation function.

internal

Automated cell type annotation for single-cell RNA sequencing data
using consensus predictions from multiple large language models (LLMs). LLMs are
artificial intelligence models trained on vast text corpora to understand and
generate human-like text. This package integrates with 'Seurat' objects and
provides uncertainty quantification for annotations. Supports various LLM
providers including 'OpenAI', 'Anthropic', and 'Google'. The package leverages
these models through their respective APIs (Application Programming Interfaces)
<https://platform.openai.com/docs>, <https://docs.anthropic.com/>, and
<https://ai.google.dev/gemini-api/docs>.
For details see Yang et al. (2025) <doi:10.1101/2025.04.10.647852>.

Chen Yang

mLLMCelltype

Cell Type Annotation Using Large Language Models

get_initial_predictions function

<dl><dt>input</dt>
<dd>Either the differential gene table or a list of genes</dd>
<dt>tissue_name</dt>
<dd>The tissue type or cell source</dd>
<dt>models</dt>
<dd>Vector of model names to use</dd>
<dt>api_keys</dt>
<dd>Named list of API keys</dd>
<dt>top_gene_count</dt>
<dd>Number of top differential genes to use</dd>
<dt>base_urls</dt>
<dd>Optional custom base URLs for API endpoints</dd></dl>

Arguments

Get initial predictions from all models — get_initial_predictions

<dl>

<dt>input</dt>
<dd>Either the differential gene table or a list of genes</dd>


<dt>tissue_name</dt>
<dd>The tissue type or cell source</dd>


<dt>models</dt>
<dd>Vector of model names to use</dd>


<dt>api_keys</dt>
<dd>Named list of API keys</dd>


<dt>top_gene_count</dt>
<dd>Number of top differential genes to use</dd>


<dt>base_urls</dt>
<dd>Optional custom base URLs for API endpoints</dd>

</dl>

get_initial_predictions: Get initial predictions from all models

Description

Usage

Value

Arguments