compendiumdb: Tools for Retrieval and Storage of Functional Genomics Data

Share:

Package for the systematic retrieval and storage of functional genomics data via a MySQL database.

Author
Umesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland <p.d.moerland@amc.uva.nl>
Date of publication
2015-10-12 11:29:15
Maintainer
Umesh Nandal <u.k.nandal@amc.uva.nl>
License
GPL (>= 2)
Version
1.0.3
URLs

View on CRAN

Man pages

checkUpdates
Check whether GSE records have been updated on GEO
compendiumdb-package
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...
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

Files in this package

compendiumdb
compendiumdb/inst
compendiumdb/inst/scripts
compendiumdb/inst/scripts/Perl
compendiumdb/inst/scripts/Perl/getAllForGSE.pl
compendiumdb/inst/scripts/Perl/loadGDS.pl
compendiumdb/inst/scripts/Perl/loadGPL.pl
compendiumdb/inst/scripts/Perl/loadAllforGSEeset.pl
compendiumdb/inst/scripts/Perl/load_notGDS.pl
compendiumdb/inst/scripts/Perl/transpose.pl
compendiumdb/inst/scripts/Perl/loadGSMeset.pl
compendiumdb/inst/scripts/Perl/parsingSoftFile_forESET.pl
compendiumdb/inst/scripts/Perl/fetchESET.pl
compendiumdb/inst/scripts/Perl/deleteAllforGPL.pl
compendiumdb/inst/scripts/Perl/expDesign.pl
compendiumdb/inst/scripts/Perl/deleteAllforGSE.pl
compendiumdb/inst/scripts/BigMac
compendiumdb/inst/scripts/BigMac/COMPENDIUM
compendiumdb/inst/scripts/BigMac/COMPENDIUM/compendiumSUB.pm
compendiumdb/inst/scripts/R
compendiumdb/inst/scripts/R/gzipScript.R
compendiumdb/inst/scripts/R/esetGeneration.R
compendiumdb/inst/scripts/R/downloadSoftFile.R
compendiumdb/inst/scripts/README
compendiumdb/inst/extdata
compendiumdb/inst/extdata/compendiumOrganismTable.txt
compendiumdb/inst/extdata/configuration.txt
compendiumdb/inst/extdata/compendiumSchema.sql
compendiumdb/inst/doc
compendiumdb/inst/doc/index.html
compendiumdb/inst/doc/compendiumdb.pdf
compendiumdb/tests
compendiumdb/tests/testthat
compendiumdb/tests/testthat/test-connectDatabase.R
compendiumdb/NAMESPACE
compendiumdb/INSTALL
compendiumdb/R
compendiumdb/R/GSEinDB.R
compendiumdb/R/removeGSE.R
compendiumdb/R/patternCheck.R
compendiumdb/R/GDSforGSE.R
compendiumdb/R/loadDataToCompendium.R
compendiumdb/R/connectDatabase.R
compendiumdb/R/GSEforGPL.R
compendiumdb/R/checkUpdates.R
compendiumdb/R/GSMdescriptions.R
compendiumdb/R/parseSampleAnnot.R
compendiumdb/R/createESET.R
compendiumdb/R/downloadGEOdata.R
compendiumdb/R/updatePhenoData.R
compendiumdb/R/tagExperiment.R
compendiumdb/R/loadDatabaseSchema.R
compendiumdb/MD5
compendiumdb/DESCRIPTION
compendiumdb/man
compendiumdb/man/GSMdescriptions.Rd
compendiumdb/man/loadDatabaseSchema.Rd
compendiumdb/man/connectDatabase.Rd
compendiumdb/man/tagExperiment.Rd
compendiumdb/man/GSEforGPL.Rd
compendiumdb/man/createESET.Rd
compendiumdb/man/GDSforGSE.Rd
compendiumdb/man/compendiumdb-package.Rd
compendiumdb/man/loadDataToCompendium.Rd
compendiumdb/man/updatePhenoData.Rd
compendiumdb/man/removeGSE.Rd
compendiumdb/man/GSEinDB.Rd
compendiumdb/man/checkUpdates.Rd
compendiumdb/man/downloadGEOdata.Rd