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AnnotationForge

Tools for building SQLite-based annotation data packages


Bioconductor version: Release (3.19)

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

Author: Marc Carlson [aut], Hervé Pagès [aut], Madelyn Carlson [ctb] ('Creating probe packages' vignette translation from Sweave to Rmarkdown / HTML), Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("AnnotationForge")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("AnnotationForge")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("AnnotationForge")
AnnotationForge: Creating select Interfaces for custom Annotation resources PDF R Script
Creating probe packages HTML R Script
Making New Organism Packages HTML R Script
SQLForge: An easy way to create a new annotation package with a standard database schema. PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Infrastructure, Software
Version 1.46.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), methods, utils, BiocGenerics(>= 0.15.10), Biobase(>= 1.17.0), AnnotationDbi(>= 1.33.14)
Imports DBI, RSQLite, XML, S4Vectors, RCurl
System Requirements
URL https://bioconductor.org/packages/AnnotationForge
Bug Reports https://github.com/Bioconductor/AnnotationForge/issues
See More
Suggests biomaRt, httr, GenomeInfoDb(>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, markdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit
Linking To
Enhances
Depends On Me
Imports Me AnnotationHubData, GOstats, ViSEAGO, GGHumanMethCancerPanelv1.db
Suggests Me AnnotationDbi, AnnotationHub
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package AnnotationForge_1.46.0.tar.gz
Windows Binary AnnotationForge_1.46.0.zip
macOS Binary (x86_64) AnnotationForge_1.46.0.tgz
macOS Binary (arm64) AnnotationForge_1.46.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/AnnotationForge
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/AnnotationForge
Bioc Package Browser https://code.bioconductor.org/browse/AnnotationForge/
Package Short Url https://bioconductor.org/packages/AnnotationForge/
Package Downloads Report Download Stats