girafe

DOI: 10.18129/B9.bioc.girafe  

Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

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

Details

biocViews	Sequencing, Software
Version	1.50.0
In Bioconductor since	BioC 2.6 (R-2.11) (13 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)
LinkingTo
Suggests	MASS, org.Mm.eg.db, RColorBrewer
SystemRequirements
Enhances	genomeIntervals
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	girafe_1.50.0.tar.gz
Windows Binary	girafe_1.50.0.zip
macOS Binary (x86_64)	girafe_1.50.0.tgz
macOS Binary (arm64)	girafe_1.50.0.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