AnnotationForge v1.12.0
Code for Building Annotation Database Packages
Provides code for generating Annotation packages and
their databases. Packages produced are intended to be
used with AnnotationDbi.
Functions in AnnotationForge
| Name | Description | |
| makeOrgPackageFromNCBI | Making an organism package from annotations available from NCBI. | |
| getProbeData_1lq | Read a 1lq file for an Affymetrix genechip | |
| generateSeqnames.db | Generates the seqnames.db package and database | |
| makeInpDb | Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects. | |
| makeChipPackage | Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package. | |
| available.db0pkgs | available.db0pkgs | |
| AnnDbPkg-maker | Creates an SQLite-based annotation package | |
| makeOrgPackage | Making an organism package from annotations available from a set of named data.frames. | |
| makeProbePackage | Make a package with probe sequence related data for microarrays | |
| getProbeDataAffy | Read a data file describing the probe sequences on an Affymetrix genechip | |
| populateDB | Populates an SQLite DB with and produces a schema definition | |
| wrapBaseDBPackages | Wrap up all the Base Databases into Packages for distribution | |
| makeDBPackage | Creates a sqlite database, and then makes an annotation package with it | |
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Details
| Collate | AnnDbPkg-maker.R sqlForge_utils.R sqlForge_baseMapBuilder.R sqlForge_schemaGen.R sqlForge_tableBuilder.R sqlForge_makeAnnPkgs.R sqlForge_wrapBaseDBPkgs.R sqlForge_seqnames.R makeProbePackage.R makeOrgPackageFromDataFrames.R makeChipPackageFromDataFrames.R NCBI_ftp.R NCBI_getters.R makeInparanoidDbs.R test_AnnotationForge_package.R |
| License | Artistic-2.0 |
| biocViews | Annotation, Infrastructure |
| VignetteBuilder | knitr |
| suggests | affy , BiocStyle , GO.db , hgu95av2.db , hom.Hs.inp.db , Homo.sapiens , human.db0 , knitr , RCurl , XML |
| depends | AnnotationDbi (>= 1.31.19) , Biobase (>= 1.17.0) , BiocGenerics (>= 0.15.10) , methods , org.Hs.eg.db , R (>= 2.7.0) , utils |
| imports | DBI , RSQLite , S4Vectors |
| Contributors | Marc Carlson, Herve Pages |
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