# Code for Building Annotation Database Packages

## Documentation for package ‘AnnotationForge’ version 1.22.2

- 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