Tools for Retrieval and Storage of Functional Genomics Data


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Documentation for package ‘compendiumdb’ version 1.0.3

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compendiumdb-package Tools for Retrieval and Storage of Functional Genomics Data
checkUpdates Check whether GSE records have been updated on GEO
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