Name	Name	Last commit message	Last commit date
parent directory ..
scripts	scripts
02_Lab_journal.ipynb	02_Lab_journal.ipynb
RA_n_Diversity_journal.R	RA_n_Diversity_journal.R
README.md	README.md
Volcano_plots_journal.R	Volcano_plots_journal.R
diff_an.yaml	diff_an.yaml

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Bat Shotgun Metagenomic Flow-work

This is the repository for supplementary materials for the upcoming publication

Differential analysis 📊

Files:

📑 02_Lab_journal.ipynb - laboratory journal with commands to reproduce pipeline
📁 scripts - folder with miscellaneous scripts used for data analysis:
- 📝 rename_files.py - script to delete _kraken_report files name for convenient data parsing further
- 📝 MaAsLin2.R - script to run MaAsLin2
- 📝 Alpha_div_calculations.R - script to calculate α-diversity
📑 Volcano_plots_journal.R - laboratory journal to plot MaAsLin2 results as volcano-plots
📑 RA_n_Diversity_journal.R - laboratory journal to plot bar-plots with relative microbial abundance; α-diversity metrics as box-plots and β-diversity metrics as PCoA plots
📑 diff_an.yaml - conda environment

Instruction:

conda env create -f diff_an.yaml

This part of work was done using: