annmap

This is the development version of annmap; for the stable release version, see annmap.

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

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Bioconductor version: Development (3.24)

annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071

Author: Tim Yates <Tim.Yates at cruk.manchester.ac.uk>

Maintainer: Chris Wirth <Christopher.Wirth at cruk.manchester.ac.uk>

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

Tim Yates. annmap: Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis. doi:10.18129/B9.bioc.annmap, R package version 1.55.1, https://bioconductor.org/packages/annmap.

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")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("annmap")

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("annmap")

annmap primer	PDF
The Annmap Cookbook	PDF
annmap installation instruction	PDF
Reference Manual	PDF
README	Text
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization
Version	1.55.1
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	GPL-2
Depends	R (>= 2.15.0), methods, GenomicRanges
Imports	DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics
System Requirements
URL	https://github.com/cruk-mi/annmap

Suggests	RUnit, rjson, Gviz
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	annmap_1.55.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	annmap_1.55.1.tgz
macOS Binary (sonoma-arm64)	annmap_1.55.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/annmap
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/annmap
Package Short Url	https://bioconductor.org/packages/annmap/
Package Downloads Report	Download Stats