CHANGES IN VERSION 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.



CHANGES IN VERSION 1.29.1
-------------------------

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



CHANGES IN VERSION 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.



CHANGES IN VERSION 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.



CHANGES IN VERSION 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'.



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.

