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ghoresh11 / twilight

All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis
GNU General Public License v3.0
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R package? #3

Closed iferres closed 2 years ago

iferres commented 2 years ago

Hi Dr Horesh, very interesting paper! Congratulations

Just a question, are you planning implement the methods into an R package? I think it would be very valuable for the pangenomics community and actually you are half the way with this repository already.

I'm a PhD student from Gregorio Iraola's Lab in Montevideo. My colleagues told me you were here in 2019, but I was in France at that moment in an internship at Institut Pasteur (working with Amine Ghozlane, I think you met him here also).

We have recently published Pagoo a tool for pangenomics analysis in R, and it would be great to have a recipe to apply some of the twilight methods you developed.

On the webpage there's a tab with what we called "Recipes" with applications of pagoo in concert with other R packages. In particular, there's one with some steps to create a phylogeny, infer lineages with Rhierbaps, and then to add this information to the pangenome object. I'm thinking on a function that could take a pan-matrix and lineage information, and classify each cluster of genes into a "Horesh category" (😎), or something like that.

What do you think?

Regards, Ignacio

ghoresh11 commented 2 years ago

Hi Ignacio,

I'm really happy you like the paper and that you find it valuable. Too bad I missed you in Montevideo, say hello to Gregorio from me :)

The script as it is essentially does what you suggest. I can imagine that it would be a nice feature to integrate it in Pagoo. Is there a way to integrate it in Pagoo in its current form? I'm now working in industry so I don't have immediate bandwidth to work on this, but I will keep in mind, especially if more people are interested.

Best Gal

iferres commented 2 years ago

Thank you for your answer, Gal.

Pagoo runs interactively in the R session, so is better to have the output already there, but you can always grab it from a file so there's no problem with that. When I find some time I will try to distil your script and make a function with that so I can write a cleaner recipe, tho. I will write you back if I achieve something to let you know, if you mind.

Bests!! Ignacio