search

EBI-Metagenomics / MGnifyR

R package for searching, downloading and analysis of EBI MGnify metagenomics data
https://ebi-metagenomics.github.io/MGnifyR/
Artistic License 2.0
19 stars 11 forks source link

Support for the (Tree)SummarizedExperiment data container #6

Closed antagomir closed 1 week ago

antagomir commented 2 years ago

I propose adding support for (Tree)SummarizedExperiment data container that is an alternative to phyloseq in the MGnifyR R package.

We can open a Pull Request?

An increasing number of microbiome data analysis tools support the TreeSummarizedExperiment (Huang et al. 2021) and MultiAssayExperiment (Ramos et al. 2017) data containers and the curatedMetagenomicData project has started to distribute the data in this format. Converters between the TreeSummarizedExperiment and phyloseq are available via the mia R/Bioc package, these are two alternative formats. We have created an online tutorial, Orchestrating Microbiome Analysis with R/Bioconductor around the TreeSummarizedExperiment framework.

beadyallen commented 2 years ago

I'm not familiar with (Tree)SummarizedExperiment, but from a quick glance it seems there's a simple phyloseq -> TSE converter function. Is there a reason that this wouldn't suffice? I think adding conversion examples in the documentation would be fine, but I'm reluctant to integrate another phyloseq equivalent before it's been proved in the field. Happy to be persuaded otherwise though :-)

antagomir commented 1 year ago

Ok, we are ready with the PR as discussed.

The new upgraded version is available at this fork: (https://github.com/microbiome/MGnifyR).

Before we open a large PR it would be good to have a chat and decide together how to take this further; to merge or to diverge.

@beadyallen looking fwd to your response!

artur-sannikov commented 3 months ago

Hi, should this be closed? We get TSE objects from MGnifyR.