NEWS

---

TCC 1.43.4

• deleted test code related with deprecated functions.
• deleted 'baySeq' dependency codes from vignette and other code.
• deleted 'baySeq' from Depends.

TCC 1.31.1

• changed default DE estimation method from exactTest to GLM-based test (glmQLFit, glmQLFTest) when using edgeR.
• removed DE estimation method for no-replicates dataset.

TCC 1.29.1

• delete 'deseq' option, since DESeq is deprecated and will be removed from Bioconductor

TCC 1.21.6

• fixed bug (order of outputs from devel version of baySeq cannot be sorted) in '.testByBayseq'.
• disabled 'samseq' option, since samr package has been removed from CRAN.
• changed design matrix used in DESeq2
• changed 'filterLowCountGenes' function processes.

TCC 1.9.3

• changed default value. Set 'test.method = "DESeq2" as default value when analyze multi-group without replicate data.
• added 'makeFCMatrix' function for generating the foldchange matrix that is used in 'simulateReadCounts' funtion.
• added function to simulate DEGs using fondchange matrix into 'simulateReadCounts' function.

TCC 1.7.13

• fixed bug in '.testBySamseq'.
• fixed bug in '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'.

TCC 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.

TCC 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.

TCC 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.

TCC 1.1.3 (2013-09-13)

• '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.

TCC 1.0.0 (2013-01-10)

• 'TCC' class was implemented as a R5 reference class. Wrapper functions with functional programming semantics were proviede.