annmap
This package is for version 3.12 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: 3.12
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 <Tim.Yates at cruk.manchester.ac.uk>
Maintainer: Chris Wirth <Christopher.Wirth at cruk.manchester.ac.uk>
citation("annmap")
):
Installation
To install this package, start R (version "4.0") 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 | |
annmap primer | |
The Annmap Cookbook | |
Reference Manual | |
NEWS | Text |
Details
biocViews | Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization |
Version | 1.32.0 |
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 |
See More
Suggests | RUnit, rjson, Gviz |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | annmap_1.32.0.tar.gz |
Windows Binary | |
macOS 10.13 (High Sierra) | annmap_1.32.0.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 3.12 | Source Archive |