AnnotationForge
This is the released version of AnnotationForge; for the devel version, see AnnotationForge.
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("AnnotationForge")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | 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. | R Script | |
| Reference Manual | ||
| NEWS | Text |
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 |
See More
| 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, 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_1.54.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/AnnotationForge/ |
| Package Short Url | https://bioconductor.org/packages/AnnotationForge/ |
| Package Downloads Report | Download Stats |