The SplicingGraphs 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.
See the Splicing graphs and RNA-seq data vignette in the package
for a gentle introduction to its use.
To access the vignette, do
click on the link to the PDF version.
The SplicingGraphs package is a reincarnation of an internal project, the SpliceGraph package, originally written by D. Bindreither, M. Carlson, and M. Morgan. SpliceGraph was never released as part of Bioconductor.
With respect to the old SpliceGraph, the scope of the new SplicingGraphs package has been reduced to focus only on the following functionalities: creating/manipulating/plotting splicing graphs, computing the bubbles and AS codes, and assigning/counting reads.
In addition to this, the old SpliceGraph package also had facilities for performing some downstream statistical analysis. They were covered in its vignette under the following topics/sections:
Significant altered alternative splice events
Modification of GLM employed in the DEXSeq package
Differential edge expression analysis
Comparison to the classic DEXSeq analysis
The SplicingGraphs vignette doesn't cover any of this and the new package provides no facilities for doing this type of downstream statistical analysis.
Author and maintainer: H. Pagès <email@example.com>
The SplicingGraphs package is a complete revamp (design and implementation) of the old SpliceGraph package (see Note above).
Heber, S., Alekseyev, M., Sze, S., Tang, H., and Pevzner, P. A. Splicing graphs and EST assembly problem Bioinformatics Date: Jul 2002 Vol: 18 Pages: S181-S188
Sammeth, M. (2009) Complete Alternative Splicing Events Are Bubbles in Splicing Graphs J. Comput. Biol. Date: Aug 2009 Vol: 16 Pages: 1117-1140
The man pages in the SplicingGraphs package are:
The SplicingGraphs class.
plotTranscripts for plotting a set of transcripts
along genomic coordinates.
sgedgesByGene for extracting the edges and their
ranges from a SplicingGraphs object.
txpath for extracting the transcript paths of a
sgedges for extracting the edges (and nodes) of a
sgraph for extracting a splicing graph as a
plottable graph-like object.
rsgedgesByGene for extracting the reduced edges
and their ranges from a SplicingGraphs object.
bubbles for computing the bubbles of a splicing graph.
assignReads for assigning reads to the edges of a
countReads for summarizing the reads assigned to
a SplicingGraphs object.
toy_genes_gff for details about the toy data included
in this package.
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