AnnotationForge

This is the released version of AnnotationForge; for the devel version, see AnnotationForge.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

Tools for building SQLite-based annotation data packages

Bioconductor version: Release (3.23)

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")):

Marc Carlson, Hervé Pagès. AnnotationForge: Tools for building SQLite-based annotation data packages. doi:10.18129/B9.bioc.AnnotationForge, R package version 1.54.0, https://bioconductor.org/packages/AnnotationForge.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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
SQLForge: An easy way to create a new annotation package with a standard database schema.	PDF	R Script
Creating probe packages	HTML	R Script
Making New Organism Packages	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Infrastructure, Software
Version	1.54.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 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

Suggests	biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, GO.db, rmarkdown, BiocStyle, knitr, BiocManager, BiocFileCache, RUnit
Linking To
Enhances
Depends On Me
Imports Me	AnnotationHubData, GGHumanMethCancerPanelv1.db, GOstats, ViSEAGO
Suggests Me	AnnotationDbi, AnnotationHub
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	AnnotationForge_1.54.0.tar.gz
Windows Binary (x86_64)	AnnotationForge_1.53.0.zip
macOS Binary (big-sur-x86_64)	AnnotationForge_1.54.0.tgz
macOS Binary (sonoma-arm64)	AnnotationForge_1.54.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AnnotationForge
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AnnotationForge
Package Short Url	https://bioconductor.org/packages/AnnotationForge/
Package Downloads Report	Download Stats