annmap

DOI: 10.18129/B9.bioc.annmap    

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

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization
Version	1.38.0
In Bioconductor since	BioC 2.11 (R-2.15) (10 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
LinkingTo
Suggests	RUnit, rjson, Gviz
SystemRequirements
Enhances
URL	https://github.com/cruk-mi/annmap
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	annmap_1.38.0.tar.gz
Windows Binary
macOS Binary (x86_64)	annmap_1.38.0.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