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Change Shell and Cloud levels

1

Hi there, I'm really enjoying Pagoo, but was wondering if there is a means of adjusting the percentage cut offs for Shell and Cloud genes, much like there is for...

alegione

Is it possible to run panaroo_2_pagoo without removing "refound_"?

2

I am working with a divergent group of organisms, so I want to keep the genes refound by panaroo because I believe the core genome is being underestimated without them....

emilywollmuth

Hello, Has anybody encountered the same issue as me? When I load the csv file, I got this error: gffs

LovaRandriantseheno

Is there a function pagoo_2_roary ?

4

Hello to the pagoo team, First, my congratulations on the great work made on the development of pagoo R library. The main question I want to put in this forum...

diaspj

Remove metadata option

3

If there is a duplicated metadata or an extra column in it there is no way to remove or modify the elements. This means that if you save an object...

g1o

Add `phylo` object as metadata

5

A tree can be considered as pangenome metadata. Provide a method to add a `phylo` object to the pangenome (with `$add_metadata()`, and make other methods be aware of it so...

iferres

See: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-12-r267#Sec8

iferres

See https://ggplot2.tidyverse.org/articles/ggplot2-in-packages.html

iferres

Implement $drop(hard = TRUE)

1

Implement an option to completely remove an organisms from the dataset. This would allow to then add metadata to available organisms without NAs needed for dropped ones. In the current...

iferres

Pangenome manipulation implies that refinement method (even manual curation) could identify miss-assignations. A gene should be able to be reassigned to other (potentially new) cluster.

iferres