Changes in version 2.23.1                        

    o   Removed coercion methods to `CountDataSet` following `DESeq` deprecation.

    o   Updated vignette to show how to use `EDASeq` with `DESeq2`.

                         Changes in version 2.3                         

    o   Added function getGeneLengthAndGCContent to compute gene length and GC-content.

    o   Updated vignette.

                         Changes in version 2.1                         

    o   Fixed bug in plotPCA: parameter k was not passed properly in SeqExpressionSet method.

    o   Fixed bug in plotQuality: trimming when reads of different lengths in same BAM/FASTQ files.

                         Changes in version 2.0                         

    o   "exprs" and "exprs<-" are now deprecated: use "counts" and "counts<-" instead (for compatibility with the DESeq class).

    o   "counts" now accesses the original counts (even after normalization) and "normCounts" accesses the normalized counts.

    o   Added the slot "normalizedCounts" to the SeqExpressionSet class: now the normalization functions will save the normalized counts in this new slot while keeping the original counts in "counts."

    o   Added option to "MDPlot" to visualize control genes in red.

    o   withinLaneNormalization and betweenLaneNormalization now always store the normalized counts in the normalizedCounts slot, even when offset=TRUE is used.

    o   Added a new method plotPCA for Principal Components Analysis (PCA) plots.

    o   Updated the vignette to reflect these changes.

    o   DESCRIPTION and NAMESPACE cleaned up.

                         Changes in version 1.9                         

    o   Added method plotRLE for Relative Log Expression (RLE) plots.

                         Changes in version 1.3                         

    o   Fixed a bug in biasPlot relative to the lwd, xlab and ylab arguments.

    o   Added a color_code option and changed the behavior of col in biasPlot.

    o   Updated CITATION file.

    o   Added an option to withinLaneNormalization and betweenLaneNormalization to return unrounded values.

    o   A new way to deal with zero counts by adding a small positive constant.

                         Changes in version 1.2                         

    o   Fixed a bug in methods plotQuality and plotNtFrequency that now allow the strand information to be missing in the SAM/BAM file.

    o   Fixed a bug in method biasPlot. It doesn't require anymore that one of the column of pData is called "conditions".

    o   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                        

    o   The read-level EDA is now based on the classes BamFileList and FastqFileList of Rsamtools. The class ShortReadSet doesn't exist anymore.

    o   Changed vignette

                       Changes in version 0.99.0                        

    o   Version number changed for submission to Bioconductor

                        Changes in version 0.0.6                        

    o   Fixed a bug in withinLaneNormalization to work with unnamed matrices

    o   Fixed a bug in biasPlot to work with a single lane experiment

    o   Added methods MDPlot and biasBoxplot

    o   Changed the vignette and added an help page for newSeqExpression function

                        Changes in version 0.0.5                        

    o   Modified coerce from SeqExpressionSet to CountDataSet to treat the two class comparison in a separate way

                        Changes in version 0.0.4                        

    o   Added Vignette

    o   Adjusted xlab in the boxplot method for signature FastqQuality

    o   Changed getOffset and setOffset<- methods in offst and offst<- for compatibility with edgeR

                        Changes in version 0.0.3                        

    o   Added CITATION file

    o   Added Help pages

    o   Added data and extdata for the examples