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

## Documentation for package ‘cosmosR’ version 1.2.0

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

## Help Pages

convert_ensembl_to_entrezid | convert gene ensembl to entrez id
convert_genesymbols_to_entrezid | convert gene symbols to entrez id
cosmos_data | Create Cosmos Data
default_CARNIVAL_options | Setting Default CARNIVAL Options
display_node_neighboorhood | display_node_neighboorhood
extract_nodes_for_ORA | Extract COSMOS nodes for ORA analysis
format_COSMOS_res | format_COSMOS_res
gmt_to_dataframe | Convert gmt file to data frame
load_tf_regulon_dorothea | load transcription factor regulon
load_tf_regulon_dorothea_omnipath | load_tf_regulon_dorothea_omnipath
metabolite_to_pubchem | Metabolite-PubChem CID Mapping
meta_network | Meta Prior Knowledge Network
omnipath_ptm | OmniPath PTMs
prepare_metabolomics_data | format COSMOS metabolic input
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.
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