Changes in Version 2.23.1 ---------------------- * Removed coercion methods to `CountDataSet` following `DESeq` deprecation. * Updated vignette to show how to use `EDASeq` with `DESeq2`. Changes in Version 2.3 ---------------------- * Added function getGeneLengthAndGCContent to compute gene length and GC-content. * Updated vignette. Changes in Version 2.1 ---------------------- * Fixed bug in plotPCA: parameter k was not passed properly in SeqExpressionSet method. * Fixed bug in plotQuality: trimming when reads of different lengths in same BAM/FASTQ files. Changes in Version 2.0 (Major update) ---------------------- * "exprs" and "exprs<-" are now deprecated: use "counts" and "counts<-" instead (for compatibility with the DESeq class). * "counts" now accesses the original counts (even after normalization) and "normCounts" accesses the normalized counts. * 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." * Added option to "MDPlot" to visualize control genes in red. * withinLaneNormalization and betweenLaneNormalization now always store the normalized counts in the normalizedCounts slot, even when offset=TRUE is used. * Added a new method plotPCA for Principal Components Analysis (PCA) plots. * Updated the vignette to reflect these changes. * DESCRIPTION and NAMESPACE cleaned up. 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