User: dago
dago • 2.6k
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Posts by dago
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... If you want to look at taxa that are differentially abundant (DA) between groups and you have repeated measure (2 time points) you need to perform a paired tests (pre vs post). It is up to you to choose the stat test you want to use. If you use a non parametric test (e.g. wilcoxon) you simply specif ...
written 6 weeks ago by
dago • 2.6k
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... That looks interesting indeed. Thank you! However, it needs to have a reference organism selected and for metagenomic data this might be a problem. I will see how it performs. ...
written 7 weeks ago by
dago • 2.6k
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... I have a list of metabolites quantified using targeted metabolomics.
I then have KEGG KOs inferred from metagenomic data.
I would like to see whether there is any KEGG pathway among the one detected that has several metabolites in my data.
In other words, I want to see what pathway is enriched in ...
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... I did not think about this. I guess I an getting used to have open source tools/db. Thanks ...
written 7 months ago by
dago • 2.6k
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... ah right, that is maybe why I could not find any tool doing that! ...
written 7 months ago by
dago • 2.6k
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... That is actually great! But I am not sure there are compounds here, just name of genes. No? ...
written 7 months ago by
dago • 2.6k
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... I saw this question has been asked here and there before.
However, I could not find a tool that does the job for me.
I want to download all pathways from KEGG including KO and compounds using R.
I would imagine creating an R object like:
$Path_1
...KO
...Compounds
$Path_2
...KO ...
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... Thank you @Amar, I appreciate your suggestions. I tried what you said as well 20.0, 20, 20.00. Always the same. I personally believe that there is an issue with Java. ...
written 14 months ago by
dago • 2.6k
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... Sorry, I did that as well, but I still get the same error. I edit my post now ...
written 14 months ago by
dago • 2.6k
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... I also posted this issue on the gatk github, sorry for the double posting ...
written 14 months ago by
dago • 2.6k
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