The goal of Infantis is to …
- pESI plasmid investigation
- gifrop with reference chromosome?
- compare to existing pESI plasmid papers?
- I think one used a pangenome approach and showed not much of a ‘core’ for the pesi plasmid?
- check for complete genomes with pESI like plasmids? can scaffold chunks?
What is special about using README.Rmd instead of just README.md?
You can include R chunks like so:
summary(cars)
#> speed dist
#> Min. : 4.0 Min. : 2.00
#> 1st Qu.:12.0 1st Qu.: 26.00
#> Median :15.0 Median : 36.00
#> Mean :15.4 Mean : 42.98
#> 3rd Qu.:19.0 3rd Qu.: 56.00
#> Max. :25.0 Max. :120.00You’ll still need to render README.Rmd regularly, to keep README.md
up-to-date. devtools::build_readme() is handy for this. You could also
use GitHub Actions to re-render README.Rmd every time you push. An
example workflow can be found here:
https://github.com/r-lib/actions/tree/master/examples.
You can also embed plots, for example:
In that case, don’t forget to commit and push the resulting figure files, so they display on GitHub.