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metagenome-atlas / Tutorial

A tutorial for Metagenome-Atlas
GNU General Public License v3.0
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Feature Request - Genecatalog analysis and updated tutorial #9

Open mladen5000 opened 1 year ago

mladen5000 commented 1 year ago

This is a bit of a vague feature request, but I was wondering if there are any plans to update or add any additional updates to this tutorial. It's been very helpful in parsing the large amounts of data generated from atlas.

SilasK commented 1 year ago

You are lucky. I am working on a Tutorial for a course this month. I pushed my work in progress to the main branch. In the file, You see my example of using the gene catalog.

https://github.com/metagenome-atlas/Tutorial/blob/new_tutorial/R/Analyze_genecatalog.Rmd

It shows how to load genes from the hdf files, combines with the annotations. Do you have some ideas?

mladen5000 commented 1 year ago

Looks great. I’m working on an analysis between a few groups, and was curious if u had any suggestions for characterizing and comparing different sets of samples

SilasK commented 1 year ago

Do you work in R or python?

I don't want to reinvent the wheel. Therfore I was looking for other R packages that would implement such a workflow.

I found tidybulk in R.

So I would suggest you to look at what they propose. I managed to create a summarized experiment from the annotated genecatalog, which is the input for tidybulk.

mladen5000 commented 1 year ago

I work in both - primarily python but hard to beat R packages for genome and statistical analysis. I didn't see that there were some updated tutorials and will check them out along with tidybulk. Thank you!

SilasK commented 10 months ago

FYI I updated the gene catalog Tutorial quite a bit.