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Bioconductor - SplicingGraphs (development version)

SplicingGraphs

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

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Bioconductor version: Development (3.22)

This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.

Author: D. Bindreither, M. Carlson, M. Morgan, H. Pagès

Maintainer: H. Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("SplicingGraphs")): Installation

To install this package, start R (version "4.5") and enter:


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

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

BiocManager::install("SplicingGraphs")

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("SplicingGraphs")
Details biocViews AlternativeSplicing, Annotation, DataRepresentation, GeneExpression, Genetics, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Visualization Version 1.49.0 In Bioconductor since BioC 2.12 (R-3.0) (12.5 years) License Artistic-2.0 Depends GenomicFeatures(>= 1.17.13), GenomicAlignments(>= 1.1.22), Rgraphviz(>= 2.3.7) Imports methods, utils, graphics, igraph, BiocGenerics, S4Vectors(>= 0.17.5), BiocParallel, IRanges(>= 2.21.2), GenomeInfoDb, GenomicRanges(>= 1.23.21), Rsamtools, graph System Requirements URL https://bioconductor.org/packages/SplicingGraphs Bug Reports https://github.com/Bioconductor/SplicingGraphs/issues See More Package Archives

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

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