Package: AnnotationForge 1.47.1

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_1.47.1.tar.gz
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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'))

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

On BioConductor:AnnotationForge-1.47.1(bioc 3.20)AnnotationForge-1.46.0(bioc 3.19)

bioconductor-package

15 exports 3.62 score 41 dependencies 20 dependents 11 mentions

Last updated 2 months agofrom:007e1ad519

Exports:available.chipdbschemas available.db0pkgs available.dbschemas getProbeData_1lq getProbeDataAffy loadAnnDbPkgIndex makeAnnDbPkg makeChipPackage makeDBPackage makeInpDb makeOrgPackage makeOrgPackageFromNCBI makeProbePackage populateDB wrapBaseDBPackages

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 bitops blob cachem cli cpp11 crayon curl DBI fastmap GenomeInfoDb GenomeInfoDbData glue httr IRanges jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig plogr png R6 RCurl rlang RSQLite S4Vectors sys UCSC.utils vctrs XML XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
available.db0pkgs	available.chipdbschemas available.db0pkgs available.dbschemas
Generates the seqnames.db package and database	generateSeqnames.db
Read a 1lq file for an Affymetrix genechip	getProbeData_1lq
Read a data file describing the probe sequences on an Affymetrix genechip	getProbeDataAffy
Create an SQLite-based annotation package	AnnDbPkgSeed 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 it	makeDBPackage
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 microarrays	makeProbePackage
Populates an SQLite DB with and produces a schema definition	popBOVINECHIPDB 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 distribution	wrapBaseDBPackages