Changes in Version 1.9
-----------------------
* Added method plotRLE for Relative Log Expression (RLE) plots.

Changes in Version 1.3
------------------------
* Fixed a bug in biasPlot relative to the lwd, xlab and ylab arguments.
* Added a color_code option and changed the behavior of col in biasPlot.
* Updated CITATION file.
* Added an option to withinLaneNormalization and betweenLaneNormalization to return unrounded values.
* A new way to deal with zero counts by adding a small positive constant.

Changes in Version 1.2
------------------------
* Fixed a bug in methods plotQuality and plotNtFrequency that now allow the strand information to be missing in the SAM/BAM file.
* Fixed a bug in method biasPlot. It doesn't require anymore that one of the column of pData is called "conditions".
* biasPlot method of SeqExpressionSet has now the argument "col" to specify the column of pData to use for color coding.

Changes in Version 0.99.1
------------------------
* The read-level EDA is now based on the classes BamFileList and FastqFileList of Rsamtools. The class ShortReadSet doesn't exist anymore.
* Changed vignette

Changes in Version 0.99.0
------------------------
* Version number changed for submission to Bioconductor

Changes in Version 0.0.6
------------------------
* Fixed a bug in withinLaneNormalization to work with unnamed matrices
* Fixed a bug in biasPlot to work with a single lane experiment
* Added methods MDPlot and biasBoxplot
* Changed the vignette and added an help page for newSeqExpression function

Changes in Version 0.0.5
------------------------
* Modified coerce from SeqExpressionSet to CountDataSet to treat the two class comparison in a separate way

Changes in Version 0.0.4
------------------------
* Added Vignette
* Adjusted xlab in the boxplot method for signature FastqQuality
* Changed getOffset and setOffset<- methods in offst and offst<- for compatibility with edgeR

Changes in Version 0.0.3
------------------------
* Added CITATION file
* Added Help pages
* Added data and extdata for the examples
