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 |