Tools for building SQLite-based annotation data packages

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Documentation for package ‘AnnotationForge’ version 1.40.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

AnnDbPkgSeed	Create an SQLite-based annotation package
AnnDbPkgSeed-class	Create an SQLite-based annotation package
available.chipdbschemas	available.db0pkgs
available.db0pkgs	available.db0pkgs
available.dbschemas	available.db0pkgs
class:AnnDbPkgSeed	Create an SQLite-based annotation package
generateSeqnames.db	Generates the seqnames.db package and database
getProbeDataAffy	Read a data file describing the probe sequences on an Affymetrix genechip
getProbeData_1lq	Read a 1lq file for an Affymetrix genechip
loadAnnDbPkgIndex	Create an SQLite-based annotation package
makeAnnDbPkg	Create an SQLite-based annotation package
makeAnnDbPkg-method	Create an SQLite-based annotation package
makeChipPackage	Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.
makeDBPackage	Creates a sqlite database, and then makes an annotation package with it
makeInpDb	Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects.
makeOrgPackage	Making an organism package from annotations available from a set of named data.frames.
makeOrgPackageFromNCBI	Make an organism package from annotations available from NCBI.
makeProbePackage	Make a package with probe sequence related data for microarrays
popBOVINECHIPDB	Populates an SQLite DB with and produces a schema definition
popBOVINEDB	Populates an SQLite DB with and produces a schema definition
popCANINECHIPDB	Populates an SQLite DB with and produces a schema definition
popCANINEDB	Populates an SQLite DB with and produces a schema definition
popCHICKENCHIPDB	Populates an SQLite DB with and produces a schema definition
popCHICKENDB	Populates an SQLite DB with and produces a schema definition
popECOLICHIPDB	Populates an SQLite DB with and produces a schema definition
popECOLIDB	Populates an SQLite DB with and produces a schema definition
popFLYCHIPDB	Populates an SQLite DB with and produces a schema definition
popFLYDB	Populates an SQLite DB with and produces a schema definition
popHUMANCHIPDB	Populates an SQLite DB with and produces a schema definition
popHUMANDB	Populates an SQLite DB with and produces a schema definition
popMALARIADB	Populates an SQLite DB with and produces a schema definition
popMOUSECHIPDB	Populates an SQLite DB with and produces a schema definition
popMOUSEDB	Populates an SQLite DB with and produces a schema definition
popPIGCHIPDB	Populates an SQLite DB with and produces a schema definition
popPIGDB	Populates an SQLite DB with and produces a schema definition
popRATCHIPDB	Populates an SQLite DB with and produces a schema definition
popRATDB	Populates an SQLite DB with and produces a schema definition
populateDB	Populates an SQLite DB with and produces a schema definition
popWORMCHIPDB	Populates an SQLite DB with and produces a schema definition
popWORMDB	Populates an SQLite DB with and produces a schema definition
popYEASTDB	Populates an SQLite DB with and produces a schema definition
popYEASTNCBIDB	Populates an SQLite DB with and produces a schema definition
popZEBRAFISHCHIPDB	Populates an SQLite DB with and produces a schema definition
popZEBRAFISHDB	Populates an SQLite DB with and produces a schema definition
wrapBaseDBPackages	Wrap up all the Base Databases into Packages for distribution