# COSMOS (Causal Oriented Search of Multi-Omic Space)

## Documentation for package ‘cosmosR’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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