SplicingGraphs-package: Create, manipulate, visualize splicing graphs, and assign...

In Bioconductor/SplicingGraphs: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

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

Description

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.

Details

See the Splicing graphs and RNA-seq data vignette in the package for a gentle introduction to its use. To access the vignette, do browseVignettes("SplicingGraphs"), then click on the link to the PDF version.

Note

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:

• Experimental design

• 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(s)

Author and maintainer: H. Pagès <[e-mail]>

The SplicingGraphs package is a complete revamp (design and implementation) of the old SpliceGraph package (see Note above).

References

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

See Also

The man pages in the SplicingGraphs package are:

1. The SplicingGraphs class.

2. plotTranscripts for plotting a set of transcripts along genomic coordinates.

3. sgedgesByGene for extracting the edges and their ranges from a SplicingGraphs object.

4. txpath for extracting the transcript paths of a splicing graph.

5. sgedges for extracting the edges (and nodes) of a splicing graph.

6. sgraph for extracting a splicing graph as a plottable graph-like object.

7. rsgedgesByGene for extracting the reduced edges and their ranges from a SplicingGraphs object.

8. bubbles for computing the bubbles of a splicing graph.

9. assignReads for assigning reads to the edges of a SplicingGraphs object.

10. countReads for summarizing the reads assigned to a SplicingGraphs object.

11. toy_genes_gff for details about the toy data included in this package.

Examples

if (interactive()) {
  ## Access the "Splicing graphs and RNA-seq data" vignette with:
  browseVignettes("SplicingGraphs")
}

Bioconductor/SplicingGraphs documentation built on Nov. 3, 2024, 8:11 a.m.