girafe

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 yahoo.de>

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

Installation

To install this package, start R (version "4.4") 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")
Genome intervals and read alignments for functional exploration PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Sequencing, Software
Version 1.56.0
In Bioconductor since BioC 2.6 (R-2.11) (14.5 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), pwalign, graphics, grDevices, stats, utils, IRanges(>= 2.13.12)
System Requirements
URL
See More
Suggests MASS, org.Mm.eg.db, RColorBrewer
Linking To
Enhances genomeIntervals
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package girafe_1.56.0.tar.gz
Windows Binary girafe_1.56.0.zip
macOS Binary (x86_64) girafe_1.56.0.tgz
macOS Binary (arm64) girafe_1.56.0.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