girafe

This is the development version of girafe; for the stable release version, see girafe.

Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: Development (3.18)

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 (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("girafe")

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("girafe")

Genome intervals and read alignments for functional exploration	PDF	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Sequencing, Software
Version	1.53.0
In Bioconductor since	BioC 2.6 (R-2.11) (13.5 years)
License	Artistic-2.0
Depends	R (>= 2.10.0), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.25), Rsamtools(>= 1.31.2), intervals (>= 0.13.1), ShortRead(>= 1.37.1), genomeIntervals(>= 1.25.1), grid
Imports	methods, Biobase, Biostrings(>= 2.47.6), graphics, grDevices, stats, utils, IRanges(>= 2.13.12)
Linking To
Suggests	MASS, org.Mm.eg.db, RColorBrewer
System Requirements
Enhances	genomeIntervals
URL

Depends On Me
Imports Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	girafe_1.53.0.tar.gz
Windows Binary	girafe_1.53.0.zip
macOS Binary (x86_64)	girafe_1.53.0.tgz
macOS Binary (arm64)	girafe_1.53.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/girafe
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/girafe
Bioc Package Browser	https://code.bioconductor.org/browse/girafe/
Package Short Url	https://bioconductor.org/packages/girafe/
Package Downloads Report	Download Stats