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Data Sets and Analyses

  • ch_and_pp (Caldwell House and Passion Puddle)
  • PM_Year1 (Princeton Meadows Year 1)
  • PM_Year2 (Princeton Meadows Year 2)
  • core_microbiomes (include data from sets above plus Huang et al, 2020 datasets)
  • evolution_analysis (includes data from rice and Arabidopsis studies)
  • other_figures (code to create NJ map figure)
  • plastid_ratio_analysis (code used to analyze DAB t0 reads)
  • data-* (figures and files used in manuscript)
  • q2_analysis_using_R.R (R functions used to analyze data)

Workflow

  • upload fastq libraries
  • use q2 to process fastq libraries and generate feature tables, diversity metrics, taxa barplots
  • use R to analyze q2 output and create visualizations
  • use R to perform differential abundance analysis using ALDEx2

Citation

If this was helpful please cite:

Acosta, K., Xu, J., Gilbert, S., Denison, E., Brinkman, T., Lebeis, S. and Lam, E., 2020. Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome. PloS one, 15(2), p.e0228560.