Tools for Storage and Retrieval of Gene Expession Data


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Documentation for package ‘compendiumdb’ version 0.1.0

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compendiumdb-package A database and R package for storing and analyzing gene expression data
compendiumdb A database and R package for storing and analyzing gene expression data
connectDatabase Create connection with the MySQL compendium database
createESET Create a Bioconductor ExpressionSet
downloadGEOdata Download a GSE from GEO
GDSforGSE Retrieve the GDS ID for a given GSE ID
GSEforGPL Retrieve the GSE ID for a given GPL ID
GSEinDB Check presence of GSEs in compendium database
GSMdescriptions List sample annotation of samples in an experiment
loadDatabaseSchema Load the compendium database schema
loadDataToCompendium Load GSE into the compendium database
removeGSE Remove series record from compendium database
tagExperiment Tag an experiment with text labels
updatePhenoData Update the phenotypic data of a set of samples