Package index • labyrinth

All functions

activation_rate(): Calculate the next-time ACT activation rate

alias2SymbolUsingNCBI(): Convert Gene Aliases to Official Gene Symbols

assert_dgCMatrix(): Check if the sparse matrix valid

disease_ids: Disease MeSH identifiers

disease_impact_score(): Get disease impact score

drug_annot: Drug annotation dataset

gene_disease: Gene-disease associations

get_neighbors(): Get neighboring nodes in a graph (adjacency matrix)

gradient(): Compute gradient of Spreadgram

graph: A small example implemented from Anderson (1983)

is.dgCMatrix(): Check if a matrix is `dgCMatrix` class

labyrinth-package labyrinth: Labyrinth: A Simulation of Knowledge Networks

load_data(): Load External Data

mesh_annot: MeSH annotation data

mesh_hierarchy: MeSH hierarchy network

mesh_synonyms: MeSH synonyms

ncbi_info: NCBI Gene Information

ppi: Protein-protein interaction network

predict_drug(): Predict drug response scores based on disease weights

random_walk(): Graph diffusion using a Markov random walk

sigmoid(): Sigmoid function of Spreadgram

speech: A portion of the phonological network examined in Vitevitch (2008).

spread_gram(): Simulate spreading activation in a network (Main function)

spread_gram_1(): Simulate spreading activation in a network (Only once)

transfer_activation(): Calculate the received activation in Spreading Activation (f)

update_gene_symbol(): Update gene symbol using NCBI Entrez Gene