COSMOS (Causal Oriented Search of Multi-Omic Space)
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Documentation for package ‘cosmosR’ version 1.15.0
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| compress_same_children | Compress Network by Merging Nodes with Identical Children |
| cosmos_data | Create Cosmos Data |
| decompress_solution_network | Decompress Solution Network |
| decoupleRnival | DecoupleRnival |
| default_CARNIVAL_options | Setting Default CARNIVAL Options |
| display_node_neighboorhood | display_node_neighboorhood |
| extract_nodes_for_ORA | Extract COSMOS nodes for ORA analysis |
| filter_incohrent_TF_target | filter_incohrent_TF_target |
| format_COSMOS_res | format_COSMOS_res |
| gmt_to_dataframe | Convert gmt file to data frame |
| HMDB_mapper_vec | Toy Input Transcription Data Set |
| load_tf_regulon_dorothea | load transcription factor regulon |
| meta_network | Meta Prior Knowledge Network |
| meta_network_cleanup | meta_network_cleanup |
| prepare_metab_inputs | add metabolic compartment and metab__ prefix to metabolite IDs |
| preprocess_COSMOS_metabolism_to_signaling | Preprocess COSMOS Inputs For Metabolism to Signaling |
| preprocess_COSMOS_signaling_to_metabolism | Preprocess COSMOS Inputs For Signaling to Metabolism |
| print.cosmos_data | Print Cosmos Data Summary Print a summary of cosmos data. |
| reduce_solution_network | reduce_solution_network |
| run_COSMOS_metabolism_to_signaling | run COSMOS metabolism to signaling |
| run_COSMOS_signaling_to_metabolism | run COSMOS signaling to metabolism |
| toy_metabolic_input | Toy Metabolic Input Data |
| toy_network | Toy Input Network |
| toy_RNA | Toy Input Transcription Data Set |
| toy_signaling_input | Toy Signaling Input |