AnnotationForge

DOI: 10.18129/B9.bioc.AnnotationForge    

Tools for building SQLite-based annotation data packages

Bioconductor version: Release (3.13)

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

Author: Marc Carlson, Hervé Pagès

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Annotation, Infrastructure, Software
Version	1.34.1
In Bioconductor since	BioC 2.11 (R-2.15) (9 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
LinkingTo
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
SystemRequirements
Enhances
URL	https://bioconductor.org/packages/AnnotationForge
BugReports	https://github.com/Bioconductor/AnnotationForge/issues
Depends On Me
Imports Me	AnnotationHubData, GGHumanMethCancerPanelv1.db, GOstats, ViSEAGO
Suggests Me	AnnotationDbi, AnnotationHub
Links To Me
Build Report

Package Archives

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

Source Package	AnnotationForge_1.34.1.tar.gz
Windows Binary	AnnotationForge_1.34.1.zip
macOS 10.13 (High Sierra)	AnnotationForge_1.34.1.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
Old Source Packages for BioC 3.13	Source Archive