AnnotationForge: Code for Building Annotation Database Packages

Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AnnotationForge")
AuthorMarc Carlson, Herve Pages
Bioconductor views Annotation Infrastructure
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.18.0

View on Bioconductor

Functions

AnnDbPkgSeed Man page
AnnDbPkgSeed-class Man page
available.chipdbschemas Man page
available.db0pkgs Man page
available.dbschemas Man page
class:AnnDbPkgSeed Man page
generateSeqnames.db Man page
getProbeData_1lq Man page
getProbeDataAffy Man page
loadAnnDbPkgIndex Man page
makeAnnDbPkg Man page
makeAnnDbPkg,AnnDbPkgSeed-method Man page
makeAnnDbPkg,character-method Man page
makeAnnDbPkg,list-method Man page
makeChipPackage Man page
makeDBPackage Man page
makeInpDb Man page
makeOrgPackage Man page
makeOrgPackageFromNCBI Man page
makeProbePackage Man page
popBOVINECHIPDB Man page
popBOVINEDB Man page
popCANINECHIPDB Man page
popCANINEDB Man page
popCHICKENCHIPDB Man page
popCHICKENDB Man page
popECOLICHIPDB Man page
popECOLIDB Man page
popFLYCHIPDB Man page
popFLYDB Man page
popHUMANCHIPDB Man page
popHUMANDB Man page
popMALARIADB Man page
popMOUSECHIPDB Man page
popMOUSEDB Man page
popPIGCHIPDB Man page
popPIGDB Man page
popRATCHIPDB Man page
popRATDB Man page
populateDB Man page
popWORMCHIPDB Man page
popWORMDB Man page
popYEASTDB Man page
popYEASTNCBIDB Man page
popZEBRAFISHCHIPDB Man page
popZEBRAFISHDB Man page
wrapBaseDBPackages Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/NCBI_getters.R R/makeAnnDbPkg.R R/makeChipPackageFromDataFrames.R R/makeInparanoidDbs.R R/makeOrgPackage.R R/makeOrgPackageFromNCBI.R R/makeProbePackage.R R/sqlForge_baseMapBuilder.R R/sqlForge_makeAnnPkgs.R R/sqlForge_schemaGen.R R/sqlForge_seqnames.R R/sqlForge_tableBuilder.R R/sqlForge_utils.R R/sqlForge_wrapBaseDBPkgs.R R/test_AnnotationForge_package.R
build
build/vignette.rds
inst
inst/AnnDbPkg-templates
inst/AnnDbPkg-templates/ARABIDOPSIS.DB
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/DESCRIPTION
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/NAMESPACE
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/R
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/R/zzz.R
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/inst
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/inst/extdata
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ARACYC.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ARACYCENZYME.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/BASE.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/CHR.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ENTREZID.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ENZYME2TAIR.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/GO.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/GO2ALLTAIRS.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/PATH.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/PATH2TAIR.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/PMID.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/PMID2TAIR.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/tests
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/tests/runalltests.R
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/tests/unit
inst/AnnDbPkg-templates/ARABIDOPSIS.DB/tests/unit/test.R
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/DESCRIPTION
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/NAMESPACE
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/R
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/R/zzz.R
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/inst
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/inst/extdata
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ACCNUM.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ARACYC.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ARACYCENZYME.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/BASE.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/CHR.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ENZYME2PROBE.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/GO.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/GO2ALLPROBES.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/GO2PROBE.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/PATH.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/PATH2PROBE.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/PMID.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/PMID2PROBE.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/runalltests.R
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/runalltests.Rout.save
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/unit
inst/AnnDbPkg-templates/ARABIDOPSISCHIP.DB/tests/unit/test.R
inst/AnnDbPkg-templates/BASEPKG.DB
inst/AnnDbPkg-templates/BASEPKG.DB/DESCRIPTION
inst/AnnDbPkg-templates/BASEPKG.DB/NAMESPACE
inst/AnnDbPkg-templates/BASEPKG.DB/inst
inst/AnnDbPkg-templates/BASEPKG.DB/inst/extdata
inst/AnnDbPkg-templates/BASEPKG.DB/man
inst/AnnDbPkg-templates/BASEPKG.DB/man/BASE.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB
inst/AnnDbPkg-templates/COELICOLOR.DB/DESCRIPTION
inst/AnnDbPkg-templates/COELICOLOR.DB/NAMESPACE
inst/AnnDbPkg-templates/COELICOLOR.DB/R
inst/AnnDbPkg-templates/COELICOLOR.DB/R/zzz.R
inst/AnnDbPkg-templates/COELICOLOR.DB/inst
inst/AnnDbPkg-templates/COELICOLOR.DB/inst/extdata
inst/AnnDbPkg-templates/COELICOLOR.DB/man
inst/AnnDbPkg-templates/COELICOLOR.DB/man/ACCNUM.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/ALIAS2EG.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/BASE.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/CHR.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/GO.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/GO2ALLEGS.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/LOCUSTAG.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/PATH.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/PMID.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/PROTEINGI.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/COELICOLOR.DB/tests
inst/AnnDbPkg-templates/COELICOLOR.DB/tests/runalltests.R
inst/AnnDbPkg-templates/COELICOLOR.DB/tests/unit
inst/AnnDbPkg-templates/COELICOLOR.DB/tests/unit/test.R
inst/AnnDbPkg-templates/GO.DB
inst/AnnDbPkg-templates/GO.DB/DESCRIPTION
inst/AnnDbPkg-templates/GO.DB/NAMESPACE
inst/AnnDbPkg-templates/GO.DB/R
inst/AnnDbPkg-templates/GO.DB/R/zzz.R
inst/AnnDbPkg-templates/GO.DB/inst
inst/AnnDbPkg-templates/GO.DB/inst/extdata
inst/AnnDbPkg-templates/GO.DB/man
inst/AnnDbPkg-templates/GO.DB/man/BASE.Rd
inst/AnnDbPkg-templates/GO.DB/man/BPANCESTOR.Rd
inst/AnnDbPkg-templates/GO.DB/man/BPCHILDREN.Rd
inst/AnnDbPkg-templates/GO.DB/man/BPOFFSPRING.Rd
inst/AnnDbPkg-templates/GO.DB/man/BPPARENTS.Rd
inst/AnnDbPkg-templates/GO.DB/man/CCANCESTOR.Rd
inst/AnnDbPkg-templates/GO.DB/man/CCCHILDREN.Rd
inst/AnnDbPkg-templates/GO.DB/man/CCOFFSPRING.Rd
inst/AnnDbPkg-templates/GO.DB/man/CCPARENTS.Rd
inst/AnnDbPkg-templates/GO.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/GO.DB/man/MFANCESTOR.Rd
inst/AnnDbPkg-templates/GO.DB/man/MFCHILDREN.Rd
inst/AnnDbPkg-templates/GO.DB/man/MFOFFSPRING.Rd
inst/AnnDbPkg-templates/GO.DB/man/MFPARENTS.Rd
inst/AnnDbPkg-templates/GO.DB/man/OBSOLETE.Rd
inst/AnnDbPkg-templates/GO.DB/man/SYNONYM.Rd
inst/AnnDbPkg-templates/GO.DB/man/TERM.Rd
inst/AnnDbPkg-templates/GO.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/INPARANOID.DB
inst/AnnDbPkg-templates/INPARANOID.DB/DESCRIPTION
inst/AnnDbPkg-templates/INPARANOID.DB/NAMESPACE
inst/AnnDbPkg-templates/INPARANOID.DB/R
inst/AnnDbPkg-templates/INPARANOID.DB/R/zzz.R
inst/AnnDbPkg-templates/INPARANOID.DB/inst
inst/AnnDbPkg-templates/INPARANOID.DB/inst/extdata
inst/AnnDbPkg-templates/INPARANOID.DB/man
inst/AnnDbPkg-templates/INPARANOID.DB/man/BASE.Rd
inst/AnnDbPkg-templates/INPARANOID.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/INPARANOID.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/INPARANOID.DB/man/ORGVSORGMAP.Rd
inst/AnnDbPkg-templates/INPARANOID.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/KEGG.DB
inst/AnnDbPkg-templates/KEGG.DB/DESCRIPTION
inst/AnnDbPkg-templates/KEGG.DB/LICENSE
inst/AnnDbPkg-templates/KEGG.DB/NAMESPACE
inst/AnnDbPkg-templates/KEGG.DB/R
inst/AnnDbPkg-templates/KEGG.DB/R/zzz.R
inst/AnnDbPkg-templates/KEGG.DB/inst
inst/AnnDbPkg-templates/KEGG.DB/inst/extdata
inst/AnnDbPkg-templates/KEGG.DB/man
inst/AnnDbPkg-templates/KEGG.DB/man/BASE.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/ENZYMEID2GO.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/EXTID2PATHID.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/GO2ENZYMEID.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/PATHID2EXTID.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/PATHID2NAME.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/PATHNAME2ID.Rd
inst/AnnDbPkg-templates/KEGG.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/MALARIA.DB
inst/AnnDbPkg-templates/MALARIA.DB/DESCRIPTION
inst/AnnDbPkg-templates/MALARIA.DB/NAMESPACE
inst/AnnDbPkg-templates/MALARIA.DB/R
inst/AnnDbPkg-templates/MALARIA.DB/R/zzz.R
inst/AnnDbPkg-templates/MALARIA.DB/inst
inst/AnnDbPkg-templates/MALARIA.DB/inst/extdata
inst/AnnDbPkg-templates/MALARIA.DB/man
inst/AnnDbPkg-templates/MALARIA.DB/man/ALIAS2ORF.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/BASE.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/GO.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/GO2ALLORFS.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/PATH.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/MALARIA.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/MALARIA.DB/tests
inst/AnnDbPkg-templates/MALARIA.DB/tests/runalltests.R
inst/AnnDbPkg-templates/MALARIA.DB/tests/unit
inst/AnnDbPkg-templates/MALARIA.DB/tests/unit/test.R
inst/AnnDbPkg-templates/NCBICHIP.DB
inst/AnnDbPkg-templates/NCBICHIP.DB/DESCRIPTION
inst/AnnDbPkg-templates/NCBICHIP.DB/NAMESPACE
inst/AnnDbPkg-templates/NCBICHIP.DB/R
inst/AnnDbPkg-templates/NCBICHIP.DB/R/zzz.R
inst/AnnDbPkg-templates/NCBICHIP.DB/inst
inst/AnnDbPkg-templates/NCBICHIP.DB/inst/extdata
inst/AnnDbPkg-templates/NCBICHIP.DB/man
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ACCNUM.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ALIAS2PROBE.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/BASE.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHR.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ENSEMBL.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ENTREZID.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/FLYBASE.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/FLYBASECG.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/GO.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/MAP.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/MGI.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/OMIM.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/PATH.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/PFAM.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/PMID.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/PROSITE.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/UNIGENE.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/UNIPROT.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/WORMBASE.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/ZFIN.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/NCBICHIP.DB/tests
inst/AnnDbPkg-templates/NCBICHIP.DB/tests/runalltests.R
inst/AnnDbPkg-templates/NCBICHIP.DB/tests/runalltests.Rout.save
inst/AnnDbPkg-templates/NCBICHIP.DB/tests/unit
inst/AnnDbPkg-templates/NCBICHIP.DB/tests/unit/test.R
inst/AnnDbPkg-templates/NCBIORG.DB
inst/AnnDbPkg-templates/NCBIORG.DB/DESCRIPTION
inst/AnnDbPkg-templates/NCBIORG.DB/NAMESPACE
inst/AnnDbPkg-templates/NCBIORG.DB/R
inst/AnnDbPkg-templates/NCBIORG.DB/R/zzz.R
inst/AnnDbPkg-templates/NCBIORG.DB/inst
inst/AnnDbPkg-templates/NCBIORG.DB/inst/extdata
inst/AnnDbPkg-templates/NCBIORG.DB/man
inst/AnnDbPkg-templates/NCBIORG.DB/man/ACCNUM.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ALIAS2EG.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/BASE.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/CHR.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ENSEMBL.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ENSEMBLPROT.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ENSEMBLTRANS.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/FLYBASE.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/FLYBASECG.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/FLYBASEPROT.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/GO.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/MAP.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/MGI.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/OMIM.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/PATH.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/PFAM.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/PMID.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/PROSITE.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/UCSCKG.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/UNIGENE.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/UNIPROT.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/WORMBASE.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/ZFIN.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/NCBIORG.DB/tests
inst/AnnDbPkg-templates/NCBIORG.DB/tests/runalltests.R
inst/AnnDbPkg-templates/NCBIORG.DB/tests/unit
inst/AnnDbPkg-templates/NCBIORG.DB/tests/unit/test.R
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/DESCRIPTION
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/NAMESPACE
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/R
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/R/zzz.R
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/inst
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/inst/extdata
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/man
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/man/BASE.Rd
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/NOCHIPSCHEMA.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/NOSCHEMA.DB
inst/AnnDbPkg-templates/NOSCHEMA.DB/DESCRIPTION
inst/AnnDbPkg-templates/NOSCHEMA.DB/NAMESPACE
inst/AnnDbPkg-templates/NOSCHEMA.DB/R
inst/AnnDbPkg-templates/NOSCHEMA.DB/R/zzz.R
inst/AnnDbPkg-templates/NOSCHEMA.DB/inst
inst/AnnDbPkg-templates/NOSCHEMA.DB/inst/extdata
inst/AnnDbPkg-templates/NOSCHEMA.DB/man
inst/AnnDbPkg-templates/NOSCHEMA.DB/man/BASE.Rd
inst/AnnDbPkg-templates/NOSCHEMA.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/NOSCHEMA.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/ORGANISM.DB
inst/AnnDbPkg-templates/ORGANISM.DB/DESCRIPTION
inst/AnnDbPkg-templates/ORGANISM.DB/NAMESPACE
inst/AnnDbPkg-templates/ORGANISM.DB/R
inst/AnnDbPkg-templates/ORGANISM.DB/R/zzz.R
inst/AnnDbPkg-templates/ORGANISM.DB/inst
inst/AnnDbPkg-templates/ORGANISM.DB/inst/extdata
inst/AnnDbPkg-templates/ORGANISM.DB/man
inst/AnnDbPkg-templates/ORGANISM.DB/man/ACCNUM.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/ALIAS2EG.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/BASE.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/CHR.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/GO.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/GO2ALLEGS.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/PMID.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/UNIGENE.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/ORGANISM.DB/tests
inst/AnnDbPkg-templates/ORGANISM.DB/tests/runalltests.R
inst/AnnDbPkg-templates/ORGANISM.DB/tests/unit
inst/AnnDbPkg-templates/ORGANISM.DB/tests/unit/test.R
inst/AnnDbPkg-templates/PFAM.DB
inst/AnnDbPkg-templates/PFAM.DB/DESCRIPTION
inst/AnnDbPkg-templates/PFAM.DB/NAMESPACE
inst/AnnDbPkg-templates/PFAM.DB/R
inst/AnnDbPkg-templates/PFAM.DB/R/zzz.R
inst/AnnDbPkg-templates/PFAM.DB/inst
inst/AnnDbPkg-templates/PFAM.DB/inst/extdata
inst/AnnDbPkg-templates/PFAM.DB/man
inst/AnnDbPkg-templates/PFAM.DB/man/BASE.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/FORWARDBIMAP.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/PDB.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/PDB2AC.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/REVERSEBIMAP.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/SCOP.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/SCOP2AC.Rd
inst/AnnDbPkg-templates/PFAM.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/YEAST.DB
inst/AnnDbPkg-templates/YEAST.DB/DESCRIPTION
inst/AnnDbPkg-templates/YEAST.DB/NAMESPACE
inst/AnnDbPkg-templates/YEAST.DB/R
inst/AnnDbPkg-templates/YEAST.DB/R/zzz.R
inst/AnnDbPkg-templates/YEAST.DB/inst
inst/AnnDbPkg-templates/YEAST.DB/inst/extdata
inst/AnnDbPkg-templates/YEAST.DB/man
inst/AnnDbPkg-templates/YEAST.DB/man/ALIAS.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/BASE.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/CHR.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/COMMON2ORF.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/DESCRIPTION.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/ENSEMBL.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/ENSEMBLPROT.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/ENSEMBLTRANS.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/ENTREZID.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/GO.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/GO2ALLORFS.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/INTERPRO.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/PATH.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/PMID.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/REJECTORF.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/SGD.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/SMART.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/UNIPROT.Rd
inst/AnnDbPkg-templates/YEAST.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/YEAST.DB/tests
inst/AnnDbPkg-templates/YEAST.DB/tests/runalltests.R
inst/AnnDbPkg-templates/YEAST.DB/tests/unit
inst/AnnDbPkg-templates/YEAST.DB/tests/unit/test.R
inst/AnnDbPkg-templates/YEASTCHIP.DB
inst/AnnDbPkg-templates/YEASTCHIP.DB/DESCRIPTION
inst/AnnDbPkg-templates/YEASTCHIP.DB/NAMESPACE
inst/AnnDbPkg-templates/YEASTCHIP.DB/R
inst/AnnDbPkg-templates/YEASTCHIP.DB/R/zzz.R
inst/AnnDbPkg-templates/YEASTCHIP.DB/inst
inst/AnnDbPkg-templates/YEASTCHIP.DB/inst/extdata
inst/AnnDbPkg-templates/YEASTCHIP.DB/man
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ALIAS.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/BASE.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/CHR.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/CHRLOC.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/DESCRIPTION.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ENSEMBL.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ENZYME2PROBE.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/GO.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/GO2ALLPROBES.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/GO2PROBE.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ORF.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/PATH.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/PATH2PROBE.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/PMID.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/PMID2PROBE.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/YEASTCHIP.DB/tests
inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/runalltests.R
inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/runalltests.Rout.save
inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/unit
inst/AnnDbPkg-templates/YEASTCHIP.DB/tests/unit/test.R
inst/AnnDbPkg-templates/YEASTNCBI.DB
inst/AnnDbPkg-templates/YEASTNCBI.DB/DESCRIPTION
inst/AnnDbPkg-templates/YEASTNCBI.DB/NAMESPACE
inst/AnnDbPkg-templates/YEASTNCBI.DB/R
inst/AnnDbPkg-templates/YEASTNCBI.DB/R/zzz.R
inst/AnnDbPkg-templates/YEASTNCBI.DB/inst
inst/AnnDbPkg-templates/YEASTNCBI.DB/inst/extdata
inst/AnnDbPkg-templates/YEASTNCBI.DB/man
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ACCNUM.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ALIAS2EG.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/BASE.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/CHR.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/CHRLENGTHS.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ENZYME.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/GENENAME.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/GO.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/GO2ALLEGS.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/MAPCOUNTS.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ORF.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/ORGANISM.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/PATH.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/PMID.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/REFSEQ.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/SGD.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/SYMBOL.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/UNIPROT.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/man/_dbconn.Rd
inst/AnnDbPkg-templates/YEASTNCBI.DB/tests
inst/AnnDbPkg-templates/YEASTNCBI.DB/tests/runalltests.R
inst/AnnDbPkg-templates/YEASTNCBI.DB/tests/unit
inst/AnnDbPkg-templates/YEASTNCBI.DB/tests/unit/test.R
inst/NOTES-Herve
inst/ProbePkg-template
inst/ProbePkg-template/DESCRIPTION
inst/ProbePkg-template/NAMESPACE
inst/ProbePkg-template/R
inst/ProbePkg-template/R/zzz.R
inst/ProbePkg-template/data
inst/ProbePkg-template/man
inst/ProbePkg-template/man/@PKGNAME@.Rd
inst/TODO
inst/doc
inst/doc/MakingNewAnnotationPackages.R
inst/doc/MakingNewAnnotationPackages.Rnw
inst/doc/MakingNewAnnotationPackages.pdf
inst/doc/MakingNewOrganismPackages.R
inst/doc/MakingNewOrganismPackages.Rmd
inst/doc/MakingNewOrganismPackages.html
inst/doc/SQLForge.R
inst/doc/SQLForge.Rnw
inst/doc/SQLForge.pdf
inst/doc/makeProbePackage.R
inst/doc/makeProbePackage.Rnw
inst/doc/makeProbePackage.pdf
inst/extdata
inst/extdata/GO_finch.txt
inst/extdata/GentlemanLab
inst/extdata/GentlemanLab/ANNDBPKG-INDEX.TXT
inst/extdata/GentlemanLab/chip-batch-script.R inst/extdata/GentlemanLab/generateSchemas.R inst/extdata/GentlemanLab/org-batch-script.R
inst/extdata/HG-U95Av2_probe_tab.gz
inst/extdata/finch_info.txt
inst/extdata/hcg110_ID
inst/extdata/hgu95av2_ID
inst/extdata/inp8_Full_species_mapping
inst/extdata/inp8_metadata
inst/extdata/unigene.txt
inst/extdata/viableIDs.rda
inst/script
inst/script/fasterOrgRecipe.R inst/script/makeNoSchemaChipDb.R inst/script/makeNoSchemaDb.R inst/script/viableIDs.R
inst/seqnames-template
inst/seqnames-template/DESCRIPTION
inst/seqnames-template/NAMESPACE
inst/seqnames-template/inst
inst/seqnames-template/inst/extdata
inst/seqnames-template/inst/extdata/dataFiles
inst/seqnames-template/inst/extdata/dataFiles/Arabidopsis_thaliana.csv
inst/seqnames-template/inst/extdata/dataFiles/Caenorhabditis_elegans.csv
inst/seqnames-template/inst/extdata/dataFiles/Cyanidioschyzon_merolae.csv
inst/seqnames-template/inst/extdata/dataFiles/Drosophila_melanogaster.csv
inst/seqnames-template/inst/extdata/dataFiles/Homo_sapiens.csv
inst/seqnames-template/inst/extdata/dataFiles/Oryza_sativa.csv
inst/seqnames-template/inst/extdata/dataFiles/Populus_trichocarpa.csv
inst/seqnames-template/inst/extdata/dataFiles/Saccharomyces_cerevisiae.csv
inst/seqnames-template/inst/extdata/dataFiles/Zea_mays.csv
inst/unitTests
inst/unitTests/test_makeOrgPackage.R
man
man/AnnDbPkg-maker.Rd man/available.db0pkgs.Rd man/generateSeqnames_db.Rd man/getProbeDataAffy.Rd man/getProbeData_1lq.Rd man/makeChipPackageFromDataFrames.Rd man/makeInpDb.Rd man/makeOrgPackage.Rd man/makeOrgPackageFromNCBI.Rd man/makeProbePackage.Rd man/sqlForge-makeCHIPDB.Rd man/sqlForge-popDB.Rd man/sqlForge-wrapDBPackages.Rd
tests
tests/AnnotationForge_unit_tests.R
vignettes
vignettes/DBschema-discussion.txt
vignettes/Homo_sapiens.pdf
vignettes/MakingNewAnnotationPackages.Rnw
vignettes/MakingNewOrganismPackages.Rmd
vignettes/SQLForge.Rnw
vignettes/makeProbePackage.Rnw

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