annmap

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see annmap.

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

Bioconductor version: 3.8

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.

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 "3.5") 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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization

Version 1.24.0

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 http://annmap.cruk.manchester.ac.uk

Suggests RUnit, rjson, Gviz

Linking To

Enhances

Depends On Me

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Build Report Build Report

Package Archives

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

Source Package annmap_1.24.0.tar.gz

Windows Binary

Mac OS X 10.11 (El Capitan) annmap_1.24.0.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

Old Source Packages for BioC 3.8 Source Archive