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lefser 1.14.0

  • [Error fix] The lefserPlot function merged the duplicated labels when the truncated name of the feature is used. Now those are plotted separately.
  • [New feature] The lefserPlot function accepts the title argument that adds the barplot title.
  • [Update] The feature names of the lefserPlot outputs are re-positioned for the improved readability.
  • [Major algorithm update] Sub-sampling and bootstrap for LDA step in the lefser function is removed. Now the LDA score is calculated directly from the whole samples.

lefser 1.12.0

Significant user-visible changes

  • The checkAbundances argument in lefser() checks that data are as relative abundances and warns if otherwise (@LiNk-NY @sdgamboa, #28)
  • relativeAb helper function available to convert data (@LiNk-NY)
  • Deprecate the expr argument and use relab (short for relative abundances)
  • Add group labels to lefserPlot (@LiNk-NY #25, @asyakhl #31)
  • 'Interoperating with phyloseq' section added to the vignette (#16)

lefser 1.0.0

  • lefser is an R/Bioconductor implementation of the LEfSe method for microbiome marker discovery (https://doi.org/10.1186/gb-2011-12-6-r60)
  • LEfSe uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers in groups and sub-group blocks.
  • lefser also implements the format of the LEfSe barplot of results