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annmap

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


Bioconductor version: Release (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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

Details

biocViews Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization
Version 1.44.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 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
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Suggests RUnit, rjson, Gviz
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Package Archives

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

Source Package annmap_1.44.0.tar.gz
Windows Binary
macOS Binary (x86_64) annmap_1.44.0.tgz
macOS Binary (arm64) annmap_1.44.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/annmap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/annmap
Bioc Package Browser https://code.bioconductor.org/browse/annmap/
Package Short Url https://bioconductor.org/packages/annmap/
Package Downloads Report Download Stats