Package index • cosmosR

All functions

HMDB_mapper_vec: Toy Input Transcription Data Set

compress_same_children(): Compress Network by Merging Nodes with Identical Children

cosmos_data(): Create Cosmos Data

createLinearColors(): Create Linear Colors Based on Numeric Input

decompress_moon_result(): Decompress Moon Result

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

format_LR_ressource(): Format Ligand-Receptor Resource

get_moon_scoring_network(): Get Moon Scoring Network

gmt_to_dataframe(): Convert gmt file to data frame

load_tf_regulon_dorothea(): load transcription factor regulon

make_heatmap_color_palette(): Create Heatmap Color Palette

meta_network: Meta Prior Knowledge Network

meta_network_cleanup(): meta_network_cleanup

moon(): moon

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

reduce_solution_network_double_thresh(): reduce_solution_network_double_thresh

run_COSMOS_metabolism_to_signaling(): run COSMOS metabolism to signaling

run_COSMOS_signaling_to_metabolism(): run COSMOS signaling to metabolism

toy_RNA: Toy Input Transcription Data Set

toy_metabolic_input: Toy Metabolic Input Data

toy_network: Toy Input Network

toy_signaling_input: Toy Signaling Input

translate_column_HMDB(): Translate Column Using HMDB Mapper

translate_res(): translate_res

wide_ulm_res(): Convert ULM Results to Wide Format