Optimised human stool sample collection for multi-omic microbiota analysis R code
1 Introduction
2 Importing and preocessing data
Main figures
3 Figure 3
4 Figure 4
- 4.1 Libraries
- 4.2 Genus
  - 4.2.1 Preprocess table and convert to genus table
  - 4.2.2 MaAsLin2 on genera
5 Figure 5
6 Figure 6
Supplementary figures
7 Supp figure 1
- 7.1 Libraries
- 7.2 Rarefactipon plot
8 Supp figure 2
- 8.1 Libraries
- 8.2 Weighted unifrac plots with relative abundance
9 Supp figure 3
- 9.1 Libraries
- 9.2 16S composition
10 Supp figure 4
- 10.1 Libraries
- 10.2 Alpha diveristy plots
11 Supp figure 5
- 11.1 Libraries
- 11.2 Barchart of Genera biomarkers
12 Supp figure 6
- 12.1 Intra group variability
13 Supp figure 7
Supplementary tables
14 Supp table 2
- 14.1 Libraries
  - 14.1.1 Statistical test
15 Supp table 3
- 15.1 Libraries
  - 15.1.1 Paired wilcox tests
16 Supp table 4
- 16.1 Libraries
- 16.2 Significant results table
17 Supp table 6
- 17.1 libraries
  - 17.1.1 Statisitical tests
18 Supp table 7
19 Supp table 8
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Optimised human stool sample collection for multi-omic microbiota analysis R code

Chapter 16 Supp table 4

All significant results from maaslin2 biomarker detection of genera.

16.1 Libraries

library("DT")

16.2 Significant results table

Analysis carried out in Fig 4 production