CHANGES IN VERSION 1.6.5 ------------------------ - 'TbT' was used 'estProps' for eliminating DEGs. However, the lastest baySeq does not give 'estProps'. Changed 'TbT' using 'floorPDEG' instead of 'estProps' when baySeq does not give 'estProps'. - fixed bug in 'simulateReadCounts' function. 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.