This repository contains all the scripts (hyper-linked) to create Figures and Tables in the lefser manuscript.

Figures

• Figure 1

  • Figure 1A. CRC data analysis with lefser
  • Figure 1B. CRC data analysis with LEfSe in barplot
  • [ongoing] Figure 1C. CRC data analysis with lefser in histogram
  • [ongoing] Figure 1D. CRC data analysis with lefser in cladogram

• Figure 2
  Benchmarking using the microbiome dataset (gingival data) with a ground truth

  • Figure 2A. Enrichment results
  • Figure 2B. Differences between putative TPs and FPs at different thresholds

Supplementary Figures

• Supplementary Figure 1

  • Supplementary Figure 1A. CRC data analysis with the original algorithm
  • Supplementary Figure 1B. CRC data analysis without noise addition and bootstrap

• Supplementary Figure 2

  • Supplementary Figure 2A. Gingival data analysis with LEfSe bootstrap iterations (only 17 features)
  • Supplementary Figure 2B. Gingival data analysis comparing LEfSe bootstrap iterations and lefser (only 17 features)

• Supplementary Figure 3

  • Supplementary Figure 3A. CRC data analysis with microbiomeMarker
  • Supplementary Figure 3B. Venn diagram of the CRC data analysis results

• Supplementary Figure 4

  • Supplementary Figure 4A. Mice data analysis with lefser
  • Supplementary Figure 4B. Mice data analysis with LEfSe
  • Supplementary Figure 4C. Mice data analysis with microbiomeMarker
  • Supplementary Figure 4D. Venn diagram of the mice data analysis results

Supplementary Tables

• Supplementary Table 1. LEfSe bootstrap iteration summary with strict thresholds (data for Supplementary Figure 2)