SplicingGraphs (version 1.10.0)

SplicingGraphs-package: 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.

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")
}