Changes in version 1.19.2                        

  - Export the reads distribution with considering the precedence.

                       Changes in version 1.19.1                        

  - Update email address.

                       Changes in version 1.17.1                        

  - allow DNAStringSet for genome.

                       Changes in version 1.13.15                       

  - add normalizeTEbyLoess functions.

                       Changes in version 1.13.14                       

  - simplify the normBy and translationalEfficiency functions.

                       Changes in version 1.13.13                       

  - update translationalEfficiency with shrink method.

                       Changes in version 1.13.12                       

  - update condonBias function.

                       Changes in version 1.13.11                       

  - fix the seqlevels style issue for coverageDepth.

                       Changes in version 1.13.10                       

  - update the codonUsage

                       Changes in version 1.13.9                        

  - fix the strand issue for readsEndPlot.
  - change the output for multiple functions.

                       Changes in version 1.13.8                        

  - update vignettes.

                       Changes in version 1.13.7                        

  - add parameter removeDuplicates for codonBias.

                       Changes in version 1.13.6                        

  - fix a issue in codonUsage.
  - update the summary output for codonBias.

                       Changes in version 1.13.5                        

  - add function codonBias.

                       Changes in version 1.13.4                        

  - fix the bug for getFPKM.

                       Changes in version 1.13.3                        

  - import txdbmaker

                       Changes in version 1.13.2                        

  - fix the bug the estimatePsite did not pass ignore.seqlevelsStyle to
    assignReadingFrame function.

                       Changes in version 1.13.1                        

  - add ignore.seqlevelsStyle parameter to provide the flexibility of
    seqlevels.

                       Changes in version 1.11.1                        

  - add precedence parameter to readsDistribution

                        Changes in version 1.7.1                        

  - export readLen for estimatePsite.

                        Changes in version 1.3.4                        

  - add rmarkdown as suggest package.

                        Changes in version 1.3.3                        

  - add github action.

                        Changes in version 1.3.2                        

  - fix the issue if there is softclip in the mapping reads and the
    reads length is smaller than shfit range.

                        Changes in version 1.3.1                        

  - keep the raw counts for countReads.

                        Changes in version 1.1.6                        

  - fix the issue in shiftReads for reads width and readsEndPlot for
    seqlevels.

                        Changes in version 1.1.5                        

  - Update documentation about the R version requirement.

                        Changes in version 1.1.4                        

  - Update authorship.

                        Changes in version 1.1.3                        

  - Fix the error "CIGAR is empty after qnarrowing".

                        Changes in version 1.1.2                        

  - update vignette to fix the typos.
  - update plotTranscript to give more informative warning message.

                        Changes in version 1.1.1                        

  - update vignette by adding background colors for better understanding
    the pipeline.

                       Changes in version 0.99.91                       

  - change Y-axis lable from Frequence to Frequency for plot
    Distance2Codon.
  - update vignette.

                       Changes in version 0.99.9                        

  - reset the test_estimatePsite.

                       Changes in version 0.99.8                        

  - decrease the testing time.

                       Changes in version 0.99.6                        

  - fix the warning missing link of plot in plotTE.

                       Changes in version 0.99.5                        

  - update ggBar function to accept more colors.
  - update readsEndPlot function with shift parameter.
  - update plotDistance2Codon function with a range of plot window
  - add codonUsage function.

                       Changes in version 0.99.4                        

  - update the description in DESCRIPTION.
  - update help files.

                       Changes in version 0.99.3                        

  - change the link from AtomicList to AtomicList-class and RUVs-methods
    to RUVs.
  - shorter lines < 80 characters.
  - spead up coverageDepth

                       Changes in version 0.99.2                        

  - remove .DS_Store

                       Changes in version 0.99.1                        

  - decrease the size of the package
  - simplify and add parameter anchor for the estimatePsite function.
  - add parameter normByLibSize for function translationalEfficiency
  - add more test files.
  - update documentations.

                       Changes in version 0.99.0                        

  - Submit to Bioconductor.

                        Changes in version 0.0.6                        

  - Remove sapply.

                        Changes in version 0.0.1                        

  - Create the package.