Comments (5)
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?
from tutorial.
Looks great. Iām working on an analysis between a few groups, and was curious if u had any suggestions for characterizing and comparing different sets of samples
from tutorial.
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.
from tutorial.
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!
from tutorial.
FYI I updated the gene catalog Tutorial quite a bit.
from tutorial.
Related Issues (8)
- Broken link to view notebook HOT 2
- Specifying memory and number of jobs HOT 3
- Unable to open 'Genecatalog/protein_catalog/db' HOT 4
- How does this work on Paired-end(1 samle - 1.fq.gz and 2.fq.gz) HOT 1
- Where to find contaminant_references ? HOT 1
- Memory requirement and path for database to run metagenome-atlas HOT 5
- Host genome reference format HOT 3
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from tutorial.