CHANGES IN VERSION 0.99 ---------------------- NEW FEATURES o Initial release. CHANGES IN VERSION 0.99-1 ---------------------- o Fixed a bug in newSeqCountSet in dealing with the input experimental designs. o Fixed a bug in computing local FDR. o Add options to model the relationship between dispersion and mean expression. CHANGES IN VERSION 1.2.0-1 ---------------------- o Fixed a bug in computing local FDR. o Change the way to deal with genes with all 0 counts. Now the FDRs for these genes are assigned as 0. CHANGES IN VERSION 1.6.0 ---------------------- o Implemented methods for detecting differentially methylated loci (DML). CHANGES IN VERSION 1.7.0 ---------------------- o Added functionalities for multiple factor experimental design. Currently edgeR functions are used for glm fitting and hypothesis testing. DSS only provide functions for dispersion estimation. CHANGES IN VERSION 2.0.0 ---------------------- o Implemented methods for detecting differentially methylated regions (DMR). o Modified the algorithm for computing variances with smoothing. o Add function to detect DML for general experimental design. o Add function to detect DML for general experimental design. CHANGES IN VERSION 2.5.0 ---------------------- Modify the parallel computing part in DML testing. We now use the 'mcapply' function in 'parallel' package to implement parallelization. Note that older version of DSS (<2.4x) used the 'bplapply' function in 'BiocParallel' package. However, that function somehow has significantly reduced performance in the new release (>1.25), so we switched to mcapply. A drawback is that the progress bar cannot be displayed under the paralelle computing setting.