Package: AnnotationForge 1.49.0

Bioconductor Package Maintainer

AnnotationForge: Tools for building SQLite-based annotation data packages

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

Authors:Marc Carlson [aut], Hervé Pagès [aut], Madelyn Carlson [ctb], Bioconductor Package Maintainer [cre]

AnnotationForge_1.49.0.tar.gz
AnnotationForge_1.49.0.zip(r-4.5)AnnotationForge_1.49.0.zip(r-4.4)AnnotationForge_1.49.0.zip(r-4.3)
AnnotationForge_1.49.0.tgz(r-4.4-any)AnnotationForge_1.49.0.tgz(r-4.3-any)
AnnotationForge_1.49.0.tar.gz(r-4.5-noble)AnnotationForge_1.49.0.tar.gz(r-4.4-noble)
AnnotationForge_1.49.0.tgz(r-4.4-emscripten)AnnotationForge_1.49.0.tgz(r-4.3-emscripten)
AnnotationForge.pdf |AnnotationForge.html✨
AnnotationForge/json (API)
NEWS

# Install 'AnnotationForge' in R:
install.packages('AnnotationForge', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/annotationforge/issues

On BioConductor:AnnotationForge-1.49.0(bioc 3.21)AnnotationForge-1.48.0(bioc 3.20)

annotationinfrastructurebioconductor-packagecore-package

9.47 score 4 stars 20 packages 150 scripts 3.1k downloads 11 mentions 15 exports 42 dependencies

Last updated 2 months agofrom:9b33fc1e83. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 29 2024
R-4.5-winWARNINGNov 29 2024
R-4.5-linuxWARNINGNov 29 2024
R-4.4-winWARNINGNov 29 2024
R-4.4-macWARNINGNov 29 2024
R-4.3-winWARNINGNov 29 2024
R-4.3-macWARNINGNov 29 2024

Exports:available.chipdbschemasavailable.db0pkgsavailable.dbschemasgetProbeData_1lqgetProbeDataAffyloadAnnDbPkgIndexmakeAnnDbPkgmakeChipPackagemakeDBPackagemakeInpDbmakeOrgPackagemakeOrgPackageFromNCBImakeProbePackagepopulateDBwrapBaseDBPackages

Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6RCurlrlangRSQLiteS4VectorssysUCSC.utilsvctrsXMLXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
available.db0pkgsavailable.chipdbschemas available.db0pkgs available.dbschemas
Generates the seqnames.db package and databasegenerateSeqnames.db
Read a 1lq file for an Affymetrix genechipgetProbeData_1lq
Read a data file describing the probe sequences on an Affymetrix genechipgetProbeDataAffy
Create an SQLite-based annotation packageAnnDbPkgSeed AnnDbPkgSeed-class class:AnnDbPkgSeed loadAnnDbPkgIndex makeAnnDbPkg makeAnnDbPkg,AnnDbPkgSeed-method makeAnnDbPkg,character-method makeAnnDbPkg,list-method
Making a chip package from annotations available from data.frame of probes mapped to gene IDs and an existing org package.makeChipPackage
Creates a sqlite database, and then makes an annotation package with itmakeDBPackage
Builds an individual DB from online files at inparanoid that is in turn meant for generating Inparanoid 8 based objects.makeInpDb
Making an organism package from annotations available from a set of named data.frames.makeOrgPackage
Make an organism package from annotations available from NCBI.makeOrgPackageFromNCBI
Make a package with probe sequence related data for microarraysmakeProbePackage
Populates an SQLite DB with and produces a schema definitionpopBOVINECHIPDB popBOVINEDB popCANINECHIPDB popCANINEDB popCHICKENCHIPDB popCHICKENDB popECOLICHIPDB popECOLIDB popFLYCHIPDB popFLYDB popHUMANCHIPDB popHUMANDB popMALARIADB popMOUSECHIPDB popMOUSEDB popPIGCHIPDB popPIGDB popRATCHIPDB popRATDB populateDB popWORMCHIPDB popWORMDB popYEASTDB popYEASTNCBIDB popZEBRAFISHCHIPDB popZEBRAFISHDB
Wrap up all the Base Databases into Packages for distributionwrapBaseDBPackages