2.23.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - *强制删除方法“CountDataSet”后“DESeq”弃用。*更新装饰图案展示如何使用“EDASeq”与“DESeq2”。2.3版本的变化- - - - - - - - - - - - - - - - - - - - - - - * getGeneLengthAndGCContent计算基因长度和GC-content添加功能。*更新的装饰图案。2.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - *固定错误plotPCA:参数k不是SeqExpressionSet通过正确的方法。*固定错误plotQuality:修剪当读取不同长度的BAM / FASTQ文件相同。2.0版本的变化(重大更新)- - - - - - - - - - - - - - - - - - - - - - - *“exprs”和“exprs < -“现在弃用:使用“计数”和“计数< -”(兼容DESeq类)。*“计数”现在访问原始计数(即使正常化)和“normCounts”访问规范化。*添加槽“normalizedCounts”SeqExpressionSet类:现在归一化函数归一化计数保存新槽同时保持原来的数量“计数”。* 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