To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("girafe")
In most cases, you don't need to download the package archive at all.
girafe
Genome Intervals and Read Alignments for Functional Exploration
Bioconductor version: 3.0
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:
source("http://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 | 1.18.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) |
| License | Artistic-2.0 |
| Depends | R (>= 2.10.0), methods, BiocGenerics, S4Vectors, 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 |
| 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_1.18.0.tar.gz |
| Windows Binary | girafe_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | girafe_1.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | girafe_1.18.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
