Single Cluster Analysis

Analyze a single cluster of marker genes to determine the cell type. Note that CASSIA is designed to handle multiple clusters simultaneously, so this is just to provide a quick way to analyze a single cluster.

Example

If you're using OpenRouter as your provider, you can specify models like "openai/gpt-4o-2024-11-20" or "anthropic/claude-3.5-sonnet". Here are some model recommendations:

• Claude 3.5 Sonnet (Best performance, slightly more expensive)
  • Model ID: "anthropic/claude-3.5-sonnet"
• GPT-4o (Balanced option)
  • Model ID: "openai/gpt-4o-2024-11-20"
• Llama 3.2 (Open source, cost-effective)
  • Model ID: "meta-llama/llama-3.2-90b-vision-instruct"
• DeepseekV3 (Open source, almost free, and performance on par with gpt4o, most recommended option)
  • Model ID: "deepseek/deepseek-chat-v3-0324"
  • Model ID: "deepseek/deepseek-chat-v3-0324:free"

Example Code

# Parameters
model <- "openai/gpt-4o-2024-11-20"  # Model ID when using OpenRouter
temperature <- 0
marker_list <- c("CD3D", "CD3E", "CD2", "TRAC")
tissue <- "blood"
species <- "human"
additional_info <- NULL
provider <- "openrouter"  # or "openai", "anthropic"

# Run the analysis
result <- runCASSIA(
  model = model,
  temperature = temperature,
  marker_list = marker_list,
  tissue = tissue,
  species = species,
  additional_info = additional_info,
  provider = provider
)

# View structured output
print(result$structured_output)

# View conversation history
print(result$conversation_history)

Note: When using OpenRouter, specify the complete model ID.