To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("annmap")

In most cases, you don't need to download the package archive at all.

annmap

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

Bioconductor version: Release (2.14)

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 <tyates at picr.man.ac.uk>

Maintainer: Tim Yates <tyates at picr.man.ac.uk>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("annmap")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("annmap")

 

PDF R Script annmap installation instruction
PDF R Script annmap primer
PDF R Script The Annmap Cookbook
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization
Version 1.6.0
In Bioconductor since BioC 2.11 (R-2.15)
License GPL-2
Depends R (>= 2.15.0), methods, GenomicRanges
Imports DBI, RMySQL (>= 0.6-0), digest, Biobase, grid, lattice, Rsamtools, genefilter, IRanges, BiocGenerics
Suggests RUnit, rjson, Gviz
System Requirements
URL http://annmap.cruk.manchester.ac.uk
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source annmap_1.6.0.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) annmap_1.6.0.tgz
Mac OS X 10.9 (Mavericks)
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center