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.

Install the latest version of this package by entering the following in R:
install.packages("compendiumdb")
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

View on CRAN

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.