AnnotationForge

DOI: 10.18129/B9.bioc.AnnotationForge    

Tools for building SQLite-based annotation data packages

Bioconductor version: Release (3.12)

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>

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

Installation

To install this package, start R (version "4.0") 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 1.32.0
In Bioconductor since BioC 2.11 (R-2.15) (8 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 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_1.32.0.tar.gz
Windows Binary AnnotationForge_1.32.0.zip
macOS 10.13 (High Sierra) AnnotationForge_1.32.0.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

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