CHANGES IN VERSION 1.9.3 ------------------------- - changed default value. Set 'test.method = "DESeq2" as default value when analyze multi-group without replicate data. - add 'makeFCMatrix' function for generating the foldchange matrix that is used in 'simulateReadCounts' funtion. - add function to simulate DEGs using fondchange matrix into 'simulateReadCounts' function. CHANGES IN VERSION 1.7.13 ------------------------- - fix bug in '.testBySamseq'. - fix bug in 'simulateReadCounts'. - rewrite the R code. - 'fit0' and 'fit1' arguments were changed to 'full' and 'reduced', 'DESeq.test' arguments were deleted. - 'voom' in limma package wa added for DEG identification. - the 'test.method' for the comparison of paired two-group can be choosed from 'edger', 'deseq', 'deseq2', 'bayseq' and 'voom'. - change the mode of expression of tcc$simulation$trueDEG. '0' indicates a non-DEG and '1' indicates a DEG, only '0' and '1' are used in this field. - 'groups' argument in 'plot.TCC' function has changed to 'group'. CHANGES IN VERSION 1.5.3 ------------------------- - fixed bug in 'ROKU' that missing to treat data consists of all zero expression. CHANGES IN VERSION 1.5.1 ------------------------- - 'do_TbT' function was deleted. - 'exactTestafterTbT' function was deleted. - 'MAplot' function was deleted. - 'NBsample' function was deleted. CHANGES IN VERSION 1.3.2 ------------------------- - DESeq2 was implemented in TCC for identifying DEGs. - EBSeq was removed from TCC. - arguments of 'WAD' function were changed. - fixed bug in '.testByDeseq' that missing to treat size factors. - the strategies for DE analysis of paired two-group dataset were implemented. - add the section for describing DE analysis of paired two-group dataset into vignette. CHANGES IN VERSION 1.2.0 ------------------------- - this package was released as a Bioconductor package (previously CRAN). - WAD method for identifying DEGs was added. - ROKU method for identifying tissue-specific genes was added. - 'increment' argument of 'calcNormFactor' function was added. - 'replicates' field of TCC class was deleted. CHANGES IN VERSION 1.1.3 ------------------------- - 'generateSimulationData' function was renamed to 'simulateReadCount'. - 'names' field of TCC class was changed to 'gene_id'. - 'hypoData' was reduced to a smaller data set. - 'hypoData_mg' was created. This is the simulation dataset which consists of 1,000 genes and 9 samples. CHANGES IN VERSION 1.0.0 ------------------------- - 'TCC' class was implemented as a R5 reference class. Wrapper functions with functional programming semantics were proviede.