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Genome Intervals and Read Alignments for Functional Exploration

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("girafe")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Sequencing, Software
Version 1.56.0
In Bioconductor since BioC 2.6 (R-2.11) (14 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), pwalign, graphics, grDevices, stats, utils, IRanges(>= 2.13.12)
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Suggests MASS,, RColorBrewer
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Enhances genomeIntervals
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Follow Installation instructions to use this package in your R session.

Source Package girafe_1.56.0.tar.gz
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macOS Binary (x86_64) girafe_1.56.0.tgz
macOS Binary (arm64) girafe_1.56.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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