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