girafe
Genome Intervals and Read Alignments for Functional Exploration
Bioconductor version: Release (2.12)
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 <j.toedling at imb-mainz.de>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("girafe")
To cite this package in a publication, start R and enter:
citation("girafe")
Documentation
| R Script | Genome intervals and read alignments for functional exploration | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | HighThroughputSequencing, Sequencing, Software |
| Version | 1.12.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), methods, IRanges(>= 1.3.53), Rsamtools, ShortRead(>= 1.3.21), intervals (>= 0.13.1), genomeIntervals(>= 1.7.3), grid |
| Imports | methods, Biobase, Biostrings, BSgenome, graphics, grDevices, stats, utils, IRanges |
| Suggests | MASS, org.Mm.eg.db, RColorBrewer |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Downloads
| Package Source | girafe_1.12.0.tar.gz |
| Windows Binary | girafe_1.12.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | girafe_1.12.0.tgz |
| Package Downloads Report | Download Stats |
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