an R package to query, visualize, and expand DisGeNET data

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Documentation for package ‘disgenet2r’ version 0.99.2

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DataGeNET.DGN-class Class DataGeNET.DGN
DataGeNET.DGN-methods Obtain the raw query from DisGeNET from a 'DataGeNET.DGN' object.
DataGeNET.DGN-methods Obtain the number of unique diseases in a 'DataGeNET.DGN'.
DataGeNET.DGN-methods Obtain the number of unique genes in a 'DataGeNET.DGN'.
DataGeNET.DGN-methods Plots the content of a 'DataGeNET.DGN' object. This functions allows to create a variety of plots for 'DataGeNET.DGN' objects.
DataGeNET.Dis-methods Obtain the raw query from DisGeNET from a 'DataGeNET.DGN' object.
DataGeNET.RDF-class Class DataGeNET.RDF
disease2attribute Retrieves genes associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
disease2biologicalprocess Query for a disease or a list of diseases and generates an 'DataGeNET.RDF'
disease2cellcomponent Query for a disease or a list of diseases and generates an 'DataGeNET.RDF'
disease2compound Query for given disease(s) and generates an 'DataGeNET.RDF'
disease2disease_by_gene Retrieves disease-disease associations via shared genes and generates an 'DataGeNET.DGN'
disease2disease_by_variant Retrieves disease-disease associations via shared genes and generates an 'DataGeNET.DGN'
disease2evidence Retrieves evidences supporting the associations, for a disease, or a list of diseases, and generates an 'DataGeNET.DGN'
disease2gene Retrieves genes associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
disease2molecularfunction Query for a disease or a list of diseases and generates an 'DataGeNET.RDF'
disease2pathway Query for given disease(s) and generates an 'DataGeNET.RDF'
disease2variant Retrieves variants associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
disease_enrichment Performs an enrichment analysis on a list of genes/variants and generates an object 'DataGeNET.DGN'
extract Obtain the raw query from DisGeNET from a 'DataGeNET.DGN' object.
gene2biologicalprocess Query for given gene(s) and generates an 'DataGeNET.RDF'
gene2cellcomponent Query for given gene(s) and generates an 'DataGeNET.RDF'
gene2disease Retrieves diseases associated to a gene, or list of genes and generates an 'DataGeNET.DGN'
gene2evidence Retrieves evidences supporting a gene-disease association, for a gene, or list of genes and generates an 'DataGeNET.DGN'
gene2indication Query for given gene(s) and generates an 'DataGeNET.RDF' Given the NCBI gene identifier, retrieves the information related to drugs which interacts with the gene product and their indications and creates an object of type 'DataGeNET.RDF'.
gene2molecularfunction Query for given gene(s) and generates an 'DataGeNET.RDF'
get_disgenet_api_key Retrieves the DisGeNET API key for a user
get_disgenet_version Retrieves DisGeNET data version
get_similar_diseases Retrieves diseases similar to an input disease and generates an 'DataGeNET.DGN'
get_umls_from_vocabulary Retrieves mappings from different vocabularies associated to a disease, or list of diseases and generates an 'DataGeNET.DGN'
ndisease Obtain the number of unique diseases in a 'DataGeNET.DGN'.
ngene Obtain the number of unique genes in a 'DataGeNET.DGN'.
pathway2disease Query for given pathway(s) and generates an 'DataGeNET.RDF'
plot Plots the content of a 'DataGeNET.DGN' object. This functions allows to create a variety of plots for 'DataGeNET.DGN' objects.
pvalue_estimation Estimates the p value of the Jaccard Coefficient for pairs of diseases
variant2disease Retrieves diseases associated to a variant or list of variants and generates an 'DataGeNET.DGN'
variant2evidence Retrieves evidences supporting a gene-disease association, for a gene, or list of genes and generates an 'DataGeNET.DGN'