Disease-Gene-Variant Relations Mining from the Public Databases and Literature


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Documentation for package ‘VarfromPDB’ version 2.2.10

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aa a table of Codon-Amino Acid Abbreviations
extract_clinvar Extract the genes and variants related to a genetic disorder from ClinVar
extract_genes_orphanet Extract the genes related to a genetic disorder from Orphanet
extract_omim Extract the genes and variants related to a genetic disorder from OMIM
extract_pubmed Extract the genes and variants related to a genetic disorder from PubMed
extract_uniprot Extract the genes and variants related to a genetic disorder from UniprotKB
genes_add_pubmed Compile the disease-related genes from PubMed abstracts into the gene set from the public databases
genes_compile Compile the disease-related genes from multiple public databases
grep_split Extention for grep function
localPDB Localize the public databases including HPO, MedGen, GeneReview, HGNC, Orphanet, ClinVar and Uniprot.
pheno_extract_HPO Extract the genes related to a disease or disease alias from HPO database.
variants_compile Compile the disease-related variants from multiple public databases