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
| R Script | annmap installation instruction | |
| R Script | annmap primer | |
| R Script | The Annmap Cookbook | |
| 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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