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jianhong / ChIPpeakAnno

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update vignettes, summarizePatternInPeaks, bump to 3.38.1, etc. #37

Closed hukai916 closed 6 months ago

hukai916 commented 6 months ago

Hi Jianhong,

Just wrapped up recent updates on the vignettes and some codes. Bumped to version 3.38.1, merge-ready. Key news:

  1. update to a single unified vignettes following Bioconductor recommended style and removed the four old ones (Kai, Haibo, and Junhui work);
  2. remove oligoNucleotideEnrichment.R and incorporate it into summarizePatternInPeaks.R (Junhui and Kai work);
  3. update findMotifsInPromoterSeqs.R to reflect changes in summarizePatternInPeaks.R;
  4. update enrichmentPlot.R to be able to wrap long labels, to use constant width for bar plot, and to be able to remove label substrings;
  5. update genomicElementDistribution.R to use transcript level rather than gene level, and change default color schemes.

This version has passed "R CMD build, check, install". NAMESPACE and Rd have be updated with roxygen, DESCRIPTION and NEWS have been manually edited, so, it should be merge-ready.

Let me know if any questions,