Feature Request - Genecatalog analysis and updated tutorial about tutorial

[SilasK]

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]

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]

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]

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]

FYI I updated the gene catalog Tutorial quite a bit.