Tools for Retrieval and Storage of Functional Genomics Data


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Documentation for package ‘compendiumdb’ version 1.0.0

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compendiumdb-package Tools for Retrieval and Storage of Functional Genomics Data
compendiumdb Tools for Retrieval and Storage of Functional Genomics Data
connectDatabase Create connection with the MySQL compendium database
createESET Create a Bioconductor ExpressionSet
downloadGEOdata Download a GSE record from GEO
GDSforGSE Retrieve information about a GDS for a given GSE
GSEforGPL Retrieve information about a GSE for a given GPL
GSEinDB Retrieve information about a GSE loaded in the compendium database
GSMdescriptions List sample annotation of samples for a given GSE
loadDatabaseSchema Load the compendium database schema
loadDataToCompendium Load GSE into the compendium database
removeGSE Remove a GSE from the compendium database
tagExperiment Tag an experiment with text labels
updatePhenoData Update the phenotypic data of a GSE record