To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("girafe")
In most cases, you don't need to download the package archive at all.
girafe
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see girafe.
Genome Intervals and Read Alignments for Functional Exploration
Bioconductor version: 3.3
The package 'girafe' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.
Author: Joern Toedling, with contributions from Constance Ciaudo, Olivier Voinnet, Edith Heard, Emmanuel Barillot, and Wolfgang Huber
Maintainer: J. Toedling <jtoedling at yahoo.de>
Citation (from within R,
enter citation("girafe")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("girafe")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("girafe")
| R Script | Genome intervals and read alignments for functional exploration | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Sequencing, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (6.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.7.21), Rsamtools, intervals (>= 0.13.1), ShortRead(>= 1.3.21), genomeIntervals(>= 1.25.1), grid |
| Imports | methods, Biobase, Biostrings, graphics, grDevices, stats, utils, IRanges(>= 2.3.23) |
| LinkingTo | |
| Suggests | MASS, org.Mm.eg.db, RColorBrewer |
| SystemRequirements | |
| Enhances | genomeIntervals |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | girafe_1.24.0.tar.gz |
| Windows Binary | girafe_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.9 (Mavericks) | girafe_1.24.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/girafe/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/girafe/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
