@@ -1,13 +1,14 @@

 Package: SplicingGraphs

 Title: Create, manipulate, visualize splicing graphs, and assign RNA-seq reads

 	to them

-Version: 1.1.10

+Version: 1.1.11

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

 License: Artistic-2.0

 Description: 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.

+	the edges of a set of splicing graphs, and to summarize them in

+        different ways.

 Maintainer: H. Pages <[email protected]>

 Depends: BiocGenerics,

 	 IRanges (>= 1.17.43), GenomicRanges (>= 1.13.5), GenomicFeatures,

@@ -1,4 +1,4 @@

-%\VignetteIndexEntry{Splicing graph analysis of RNA-Seq data}

+%\VignetteIndexEntry{Splicing graphs and RNA-seq data}

 %\VignetteDepends{SplicingGraphs,TxDb.Hsapiens.UCSC.hg19.knownGene,RNAseqData.HeLa.bam.chr14,Rsamtools}

 %\VignetteKeywords{Annotation}

 %\VignettePackage{SplicingGraphs}

@@ -32,7 +32,7 @@

 \SweaveOpts{keep.source=TRUE}

-\title{Splicing graph analysis of RNA-Seq data}

+\title{Splicing graphs and RNA-seq data}

 \author{Herv\'e Pag\`es\and

   Daniel Bindreither\and

@@ -103,24 +103,6 @@ HeLa cells (\textit{Human}).

 %\cite{Anders:2010}, the approach of analyzing splicing events as

 %complete complex structure is still new. 

-[TODO: Remove the following TEMPORARY NOTE before BioC 2.12 release.]

-

-TEMPORARY NOTE: The scope of the new \Rpackage{SplicingGraphs} package

-has been reduced roughly to the following functionalities:

-creating/manipulating/plotting splicing graphs, computing the bubbles

-and AS codes, and counting reads. In particular anything in the old

-\Rpackage{SpliceGraph} package that was related to the downstream

-statistical analysis has been dropped. As a consequence the following

-topics/sections from the old \Rpackage{SpliceGraph} vignette are not

-covered in this vignette:

-\begin{itemize}

-  \item ``The experimental design''

-  \item ``Significant altered alternative splice events''

-  \item Modification of GLM employed in the \Rpackage{DEXSeq} package.

-  \item ``Differential edge expression analysis''

-  \item Comparison to the classic \Rpackage{DEXSeq} analysis.

-\end{itemize}

- 

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 \section{Splicing graphs}

@@ -12,11 +12,15 @@

   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.

+  reads to the edges of a set of splicing graphs, and to summarize them in

+  different ways.

 }

 \details{

-  TODO

+  See the \emph{Splicing graphs and RNA-seq data} vignette in the package

+  for a gentle introduction to the \pkg{SplicingGraphs} package.

+  To access the vignette, do \code{browseVignettes("SplicingGraphs")}, then

+  click on the link to the PDF version.

 }

 \author{

@@ -32,6 +36,27 @@

   Maintainer: H. Pages <[email protected]>

 }

+\note{

+  With respect to the old \pkg{SpliceGraph} package, the scope of the new

+  \pkg{SplicingGraphs} package has been reduced roughly to 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

+  package provides no facilities for doing this type of downstream statistical

+  analysis. 

+}

+

 \references{

   Heber, S., Alekseyev, M., Sze, S., Tang, H., and Pevzner, P. A. 

   \emph{Splicing graphs and EST assembly problem}

@@ -84,4 +109,10 @@

   }

 }

+\examples{

+if (interactive()) {

+  ## Access the "Splicing graphs and RNA-seq data" vignette with:

+  browseVignettes("SplicingGraphs")

+}

+}

 \keyword{package}