compendiumdb: Tools for Retrieval and Storage of Functional Genomics Data

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

AuthorUmesh K. Nandal <u.k.nandal@amc.uva.nl> and Perry D. Moerland <p.d.moerland@amc.uva.nl>
Date of publication2015-10-12 11:29:15
MaintainerUmesh Nandal <u.k.nandal@amc.uva.nl>
LicenseGPL (>= 2)
Version1.0.3
http://wiki.bioinformaticslaboratory.nl/foswiki/bin/view/BioLab/CompendiumDB

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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

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