Man pages for mLLMCelltype
Cell Type Annotation Using Large Language Models
| annotate_cell_types | Cell Type Annotation with Multi-LLM Framework |
| AnthropicProcessor | Anthropic API Processor |
| BaseAPIProcessor | Base API Processor Class |
| CacheManager | Cache Manager Class |
| calculate_simple_consensus | Calculate simple consensus without LLM |
| check_consensus | Check if consensus is reached among models |
| clean_annotation | Clean annotation text by removing prefixes and extra... |
| combine_results | Combine results from all phases of consensus annotation |
| compare_model_predictions | Compare predictions from different models |
| configure_logger | Set global logger configuration |
| create_annotation_prompt | Create prompt for cell type annotation |
| create_consensus_check_prompt | Create prompt for checking consensus among model predictions |
| create_discussion_prompt | Create prompt for additional discussion rounds |
| create_initial_discussion_prompt | Create prompt for the initial round of discussion |
| create_standardization_prompt | Create prompt for standardizing cell type names |
| custom_providers | Custom model manager for mLLMCelltype |
| DeepSeekProcessor | DeepSeek API Processor |
| dot-onAttach | Package startup message |
| dot-onLoad | Package load message |
| execute_consensus_check | Execute consensus check with retry logic |
| extract_labeled_value | Extract numeric value from line containing a label |
| facilitate_cluster_discussion | Facilitate discussion for a controversial cluster |
| filter_valid_responses | Filter out error responses from model round responses |
| find_majority_prediction | Find majority prediction from response lines |
| GeminiProcessor | Gemini API Processor |
| get_api_key | Utility functions for API key management |
| get_initial_predictions | Get initial predictions from all models |
| get_logger | Get the global logger instance |
| get_model_response | Get response from a specific model |
| get_provider | Determine provider from model name |
| GrokProcessor | Grok API Processor |
| identify_controversial_clusters | Identify controversial clusters based on consensus analysis |
| initialize_logger | Reinitialize global logger with a specific directory |
| interactive_consensus_annotation | Interactive consensus building for cell type annotation |
| list_custom_models | Get list of registered custom models |
| list_custom_providers | Get list of registered custom providers |
| logging_functions | Convenience functions for logging |
| MinimaxProcessor | Minimax API Processor |
| mllmcelltype_cache_dir | Get mLLMCelltype cache location |
| mllmcelltype_clear_cache | Clear mLLMCelltype cache |
| mLLMCelltype-package | mLLMCelltype: Cell Type Annotation Using Large Language... |
| normalize_annotation | Normalize annotation for comparison |
| normalize_cluster_gene_list | Normalize list input into a canonical cluster->genes mapping |
| OpenAIProcessor | OpenAI API Processor |
| OpenRouterProcessor | OpenRouter API Processor |
| parse_consensus_response | Parse consensus response from model |
| parse_flexible_format | Parse flexible format consensus response |
| parse_standard_format | Parse standard 4-line consensus response format |
| parse_text_predictions | Parse text-format model predictions into a named list |
| prepare_models_list | Prepare list of models to try for consensus checking |
| print_consensus_summary | Print summary of consensus results |
| process_anthropic | Process request using Anthropic models |
| process_controversial_clusters | Process controversial clusters through discussion |
| process_custom | Process request using custom provider |
| process_deepseek | Process request using DeepSeek models |
| process_gemini | Process request using Gemini models |
| process_grok | Process request using Grok models |
| process_minimax | Process request using MiniMax models |
| process_openai | Process request using OpenAI models |
| process_openrouter | Process request using OpenRouter models |
| process_qwen | Process request using Qwen models |
| process_stepfun | Process request using StepFun models |
| process_zhipu | Process request using Zhipu models |
| QwenProcessor | Qwen API Processor |
| register_custom_model | Register a custom model for a provider |
| register_custom_provider | Register a custom LLM provider |
| resolve_provider_base_url | URL Utilities for Base URL Resolution |
| select_best_prediction | Select the best prediction from consensus results |
| standardize_cell_type_names | Standardize cell type names using a language model |
| StepFunProcessor | StepFun API Processor |
| UnifiedLogger | Unified Logger for mLLMCelltype Package |
| ZhipuProcessor | Zhipu API Processor |
