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# Analysis of _pks_ in faecal metagenomes of multiple recurrent _Clostridioides difficile_ infected patients and their donors

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This project stores all the analysis scripts with descriptions, comments, figures and essential data of the manuscript by Nooij _et al_., titled 'Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients' ([_Gastroenterology_, June 2021](https://doi.org/10.1053/j.gastro.2021.06.009)).
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For a brief description of the analysis and each individual step, please check [the contents here](0_Analysis_contents.md).

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## Included software

This collection of analysis scripts is written in [R](https://www.R-project.org/), using R version 4.0.2 and [RStudio Server](https://rstudio.com/).
The scripts make use of the following packages:

| Package | Version | Reference |
| ------- | ------- | --------- |
| `knitr` | 1.30    | https://yihui.name/knitr/ |
| `rmarkdown` | 2.4 | https://CRAN.R-project.org/package=rmarkdown |
| `here`  | 0.1     | https://CRAN.R-project.org/package=here |
| `codetools` | 0.2-16 | https://CRAN.R-project.org/package=codetools |
| `tidyverse` | 1.3.0 | https://www.tidyverse.org/packages/ |
| `DT`    | 0.17    | https://rstudio.github.io/DT/ |
| `Hmisc` | 4.4-1   | https://CRAN.R-project.org/package=Hmisc |
| `corrplot` | 0.84 | https://github.com/taiyun/corrplot |
| `ggpubr` | 0.4.0  | https://rpkgs.datanovia.com/ggpubr/ |
| `cowplot` | 1.1.0 | https://wilkelab.org/cowplot/index.html |
| `viridisLite` | 0.3.0 | https://CRAN.R-project.org/package=viridisLite |
| `pheatmap` | 1.0.12 | https://CRAN.R-project.org/package=pheatmap |
| `scales`  | 1.1.1 | https://scales.r-lib.org/ |
| `esc`   | 0.5.1   | https://strengejacke.github.io/esc/ |


(For further details, please see the 'Software included' section at the bottom of each analysis step report, where R's `sessionInfo()` is printed.)

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## Licence

This project is licensed under a permissive, free and open source licence. 
That means that any part of it may be copied, used and shared.
The only requirement is that you cite this project when using substantial parts of the code.
(For details, please refer to the [license](LICENSE).)