annmap

DOI: 10.18129/B9.bioc.annmap    

This package is for version 3.15 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: 3.15

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>

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

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

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