Accompanying code to Kerckhof, Sakarika, et. al. 2021
Kerckhof FM, Sakarika M, Van Giel M, Muys M, Vermeir P, De Vrieze J, Vlaeminck SE, Rabaey K, Boon N. From Biogas and Hydrogen to Microbial Protein Through Co-Cultivation of Methane and Hydrogen Oxidizing Bacteria. Front Bioeng Biotechnol. 2021 Aug 30;9:733753. doi: 10.3389/fbioe.2021.733753. PMID: 34527661; PMCID: PMC8435580.
- RAxML we used v. 8.2.11 and visualized with iTOL
- R we used v. 4.0.4 in our preferred IDE, RStudio
- The CRAN R packages ggplot2, ggthemes, grid, gridextra, ggpubr, lawstat, readxl, dplyr, NMF
- The Phenoflow R package for flow cytometry fingerprinting and it's dependencies
| File/folder in root | Description |
|---|---|
| output_files/raxmloutput | intermediary output files for RAxML phylogenetic inference (SI Figure 1) |
| source_files | processed datafiles (not the ones in the repositories) needed to run certain scripts |
| .gitignore | file to describe which files git should not track |
| Kerckhof_Sakarika_etal_2021.Rproj | Rstudio project file |
| LICENSE | License |
| README.md | This file |
| raxml_code.sh | RAxML options used to infer phylogeny (SI Figure 1) |
| Selective_plating_results.R | Processing of selective plating results (Figure 2) |
| Amino_acid_composition.R | Code to reproduce Figure 4 and Figure 5 |