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CHANGES IN VERSION 1.37.3 ------------------------- o Removed support for baySeq since it has been deprecated o Added runComparisonShiny function CHANGES IN VERSION 1.35.1 ------------------------- o Add a function for SVA + limma differential expression analysis CHANGES IN VERSION 1.31.1 ------------------------- o Implement simulations according to the phylogenetic poisson log normal model o Implement length-varying simulations o New PhyloCompData object for phylogenetic informed simulation data o Add possible length normalization to DESeq2 and limma analyses o Add phylolm analyses CHANGES IN VERSION 1.23.1 ------------------------- o Moved vignette to Rmd CHANGES IN VERSION 1.17.1 ------------------------- o Removed support for SAMseq since samr has been removed from CRAN CHANGES IN VERSION 1.5.3 ------------------------ o Updated baySeq code to match package version 2.2.0 CHANGES IN VERSION 1.5.2 ------------------------ o Updated NBPseq code to match package version 0.3.0 CHANGES IN VERSION 1.5.1 ------------------------ o Added the number of significant genes, then number of true positives, true negatives, false positives and false negatives as evaluation criteria. o Bug fixes CHANGES IN VERSION 1.3.4 ------------------------ o Fixed documentation CHANGES IN VERSION 1.3.3 ------------------------ o Removed support for HTSDiff since it has been removed from CRAN CHANGES IN VERSION 1.3.2 ------------------------ o Fixed a bug that prevented data sets with more than 17,343 genes to be simulated (thanks to Simon Greenaway) CHANGES IN VERSION 1.3.1 ------------------------ o Updated vignette o Added citation file CHANGES IN VERSION 1.2.0 ------------------------ o Release version with Bioconductor 3.0 CHANGES IN VERSION 1.1.4 ------------------------ o Added MCC (Matthew's correlation coefficient) as evaluation measure CHANGES IN VERSION 1.1.3 ------------------------ o Fixed summarizeSyntheticDataSet to work also for non-simulated data CHANGES IN VERSION 1.1.2 ------------------------ o Added reference information for TCC (thanks to Koji Kadota) CHANGES IN VERSION 1.1.1 ------------------------ o Bug fix in EBSeq quantile normalization (thanks to Rory Kirchner) CHANGES IN VERSION 0.99.3 ------------------------- o Bug fixes CHANGES IN VERSION 0.99.2 ------------------------- o Extended the examples o Bug fixes CHANGES IN VERSION 0.99.1 ------------------------- o inclusion of an additional comparison metric, relating the gene score to the signal strength for genes expressed in only one condition o improved documentation of the compData class CHANGES IN VERSION 0.99.0 ------------------------- o identical to 0.2.0, renamed for Bioconductor submission CHANGES IN VERSION 0.2.0 ------------------------ o introduction of a new S4 class (compData) and associated functions o more examples, checks and error messages o more options for providing user-specified values in the data simulation o changed the range of the color palette in the Spearman correlation plots to [-1,1] CHANGES IN VERSION 0.1.0 ------------------------ o first version