annmap
This is the development version of annmap; for the stable release version, see annmap.
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Bioconductor version: Development (3.21)
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("annmap")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | |
| README | Text |
| NEWS | Text |
| LICENSE | Text |
Details
| biocViews | Annotation, Microarray, OneChannel, ReportWriting, Software, Transcription, Visualization |
| Version | 1.49.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 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 | https://github.com/cruk-mi/annmap |
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_1.49.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |