% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/prompt_templates.R
\name{create_reasoning_annotation_prompt}
\alias{create_reasoning_annotation_prompt}
\title{Create reasoning-aware prompt for cell type annotation}
\usage{
create_reasoning_annotation_prompt(input, tissue_name, top_gene_count = 10)
}
\arguments{
\item{input}{Either a data frame from Seurat's FindAllMarkers() or a list for each cluster
where each element is either a character vector of genes or a list containing a \code{genes} field.}

\item{tissue_name}{Tissue context for the annotation (e.g., 'human PBMC', 'mouse brain')}

\item{top_gene_count}{Number of top genes to use per cluster when input is from Seurat. Default: 10}
}
\value{
A list with \code{prompt} (formatted prompt text), \code{expected_count}
(number of clusters), and \code{gene_lists} (cluster ID to marker genes mapping).
}
\description{
Create reasoning-aware prompt for cell type annotation
}
