版本1.29.1变化- - - - - - - - - - - - - - - - - - - - - - - - - -删除“deseq”选项,因为deseq弃用和将被删除从Bioconductor 1.21.6版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -固定错误(从重击的顺序输出版本的baySeq不能排序)在“.testByBayseq”。——禁用“samseq”选项,因为samr包已被删除从凹口。-改变设计矩阵用于DESeq2改变filterLowCountGenes的功能流程。1.9.3版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - -改变了默认值。设置的考试。方法=“DESeq2”时默认值分析多群而不复制数据。——添加“makeFCMatrix”函数生成foldchange矩阵用于“simulateReadCounts”功能。——添加函数模拟使用fondchange度矩阵“simulateReadCounts”功能。版本变化1.7.13 - - - - - - - - - - - - - - - - - - - - - - - - - -固定错误“.testBySamseq”。——固定错误“simulateReadCounts”。 - rewrote 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. - '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.