AnnotationForge

DOI: 10.18129/B9.bioc.AnnotationForge    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see AnnotationForge.

Tools for building SQLite-based annotation data packages

Bioconductor version: 3.9

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 "3.6") 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	1.26.0
In Bioconductor since	BioC 2.11 (R-2.15) (7 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, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	AnnotationHubData, GGHumanMethCancerPanelv1.db, GOstats
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_1.26.0.tar.gz
Windows Binary	AnnotationForge_1.26.0.zip
Mac OS X 10.11 (El Capitan)	AnnotationForge_1.26.0.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