This package is for version 3.9 of Bioconductor;
for the stable, up-to-date release version, see
girafe.
Genome Intervals and Read Alignments for Functional Exploration
Bioconductor version: 3.9
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
“3.6”) and enter:
if (!requireNamespace("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 | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Sequencing, Software |
| Version | 1.36.0 |
| In Bioconductor since | BioC 2.6 (R-2.11) (9.5 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) |
| 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.
Read more here: Source link