annmap

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

Bioconductor version: Release (2.12)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("annmap")

Documentation

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, Bioinformatics, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization
Version 1.2.1
In Bioconductor since BioC 2.11 (R-2.16)
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
System Requirements
URL http://annmap.picr.man.ac.uk
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source annmap_1.2.1.tar.gz
Windows Binary
Mac OS X 10.6 (Snow Leopard) annmap_1.2.1.tgz
Package Downloads Report Download Stats

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