# 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.