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AnnotationForge (version 1.10.1)

Code for Building Annotation Database Packages

Description

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

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Version

Version

1.10.1

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in AnnotationForge (1.10.1)

makeOrgPackage

Making an organism package from annotations available from a set of named data.frames.
getProbeData_1lq

Read a 1lq file for an Affymetrix genechip
getProbeDataAffy

Read a data file describing the probe sequences on an Affymetrix genechip
generateSeqnames.db

Generates the seqnames.db package and database
makeProbePackage

Make a package with probe sequence related data for microarrays
makeOrgPackageFromNCBI

Making an organism package from annotations available from NCBI.
makeChipPackage

Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.
makeInpDb

Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects.
available.db0pkgs

available.db0pkgs
AnnDbPkg-maker

Creates an SQLite-based annotation package
makeDBPackage

Creates a sqlite database, and then makes an annotation package with it
wrapBaseDBPackages

Wrap up all the Base Databases into Packages for distribution
populateDB

Populates an SQLite DB with and produces a schema definition