\name{SplicingGraphs-package}
 \docType{package}
 
 \alias{SplicingGraphs-package}
 
 \title{

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

 }
 
 \description{

   The \pkg{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 \emph{Splicing graphs and RNA-seq data} vignette in the package

   for a gentle introduction to its use.

   To access the vignette, do \code{browseVignettes("SplicingGraphs")}, then
   click on the link to the PDF version.

 }
 

 \note{

   The \pkg{SplicingGraphs} package is a reincarnation of an internal project,
   the \pkg{SpliceGraph} package, originally written by D. Bindreither,
   M. Carlson, and M. Morgan. \pkg{SpliceGraph} was never released as part of
   Bioconductor.
 
   With respect to the old \pkg{SpliceGraph}, the scope of the new
   \pkg{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 \pkg{SpliceGraph} package also had facilities
   for performing some downstream statistical analysis. They were covered in
   its vignette under the following topics/sections:
   \itemize{
     \item Experimental design
     \item Significant altered alternative splice events
     \item Modification of GLM employed in the \pkg{DEXSeq} package
     \item Differential edge expression analysis
     \item Comparison to the classic \pkg{DEXSeq} analysis
   }

   The \pkg{SplicingGraphs} vignette doesn't cover any of this and the new

   package provides no facilities for doing this type of downstream statistical
   analysis. 
 }
 

 \author{

   Author and maintainer: H. Pages <[email protected]>

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

 \references{
   Heber, S., Alekseyev, M., Sze, S., Tang, H., and Pevzner, P. A. 
   \emph{Splicing graphs and EST assembly problem}
   Bioinformatics
   Date: Jul 2002
   Vol: 18
   Pages: S181-S188
 
   Sammeth, M. (2009) 
   \emph{Complete Alternative Splicing Events Are Bubbles in Splicing Graphs}
   J. Comput. Biol.
   Date: Aug 2009
   Vol: 16
   Pages: 1117-1140
 }
 
 \seealso{

   The man pages in the \pkg{SplicingGraphs} package are:

   \enumerate{
     \item The \link{SplicingGraphs} class.
 
     \item \code{\link{plotTranscripts}} for plotting a set of transcripts
           along genomic coordinates.
 

     \item \code{\link{sgedgesByGene}} for extracting the edges and their

           ranges from a SplicingGraphs object.
 
     \item \code{\link{txpath}} for extracting the transcript paths of a
           splicing graph.
 
     \item \code{\link{sgedges}} for extracting the edges (and nodes) of a
           splicing graph.
 
     \item \code{\link{sgraph}} for extracting a splicing graph as a
           plottable graph-like object.
 

     \item \code{\link{rsgedgesByGene}} for extracting the reduced edges
           and their ranges from a SplicingGraphs object.
 

     \item \code{\link{bubbles}} for computing the bubbles of a splicing graph.
 

     \item \code{\link{assignReads}} for assigning reads to the edges of a
           SplicingGraphs object.
 
     \item \code{\link{countReads}} for summarizing the reads assigned to

           a SplicingGraphs object.

 
     \item \code{\link{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")
 }
 }

 \keyword{package}