https://github.com/bartongroup/mg_t6ss_tn-seq
Analysis of Ssp4 and Ssp6 effects on Pseudomonas fluorescens using Tn-seq (Coulthurst)
Science Score: 13.0%
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Low similarity (4.9%) to scientific vocabulary
Repository
Analysis of Ssp4 and Ssp6 effects on Pseudomonas fluorescens using Tn-seq (Coulthurst)
Basic Info
- Host: GitHub
- Owner: bartongroup
- Language: R
- Default Branch: main
- Size: 23.1 MB
Statistics
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Analysis of Ssp4 and Ssp6 effects on Pseudomonas fluorescens using Tn-seq
The R code to accompany the manuscript “A widely-occurring family of pore-forming effectors broadens the impact of the Serratia Type VI secretion system” by Mark Reglinski, Quenton W. Hurst, David J. Williams, Marek Gierlinski, Alp Tegin Şahin, Katharine Mathers, Adam Ostrowski, Megan Bergkessel, Ulrich Zachariae, Samantha J. Pitt and Sarah J. Coulthurst.
Instructions
The R code in this repository uses renv and targets for reproducibility. renv is used to reproduce the R environment:
install.packages("renv")
renv::restore()
Next, the targets pipeline is invoked with the following command:
targets::tar_make()
Finally, the HTML report, including all figures, can be created with:
quarto::quarto_render("doc/report.qmd")
The HTML file will be created in folder doc.
Owner
- Name: Geoff Barton's Computational Biology Group
- Login: bartongroup
- Kind: organization
- Location: Dundee, Scotland, UK
- Website: https://www.compbio.dundee.ac.uk
- Twitter: bartongrp
- Repositories: 57
- Profile: https://github.com/bartongroup
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