User: dago

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dago2.6k
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Posts by dago

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Answer: A: Biological Replicates At Two Time Points in 16S rRNA Dataset
... 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 dago2.6k
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Comment: C: Integrate metabolomic and pathway information
... 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 dago2.6k
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Integrate metabolomic and pathway information
... 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 ...
metabolomics R kegg gene system biology written 9 weeks ago by dago2.6k • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: R: download all KEGG pathways including KO and Compounds
... I did not think about this. I guess I an getting used to have open source tools/db. Thanks ...
written 7 months ago by dago2.6k
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Comment: C: R: download all KEGG pathways including KO and Compounds
... ah right, that is maybe why I could not find any tool doing that! ...
written 7 months ago by dago2.6k
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Comment: C: R: download all KEGG pathways including KO and Compounds
... That is actually great! But I am not sure there are compounds here, just name of genes. No? ...
written 7 months ago by dago2.6k
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R: download all KEGG pathways including KO and Compounds
... 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 ...
R system_biology kegg written 7 months ago by dago2.6k • updated 7 months ago by ATpoint44k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... 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 dago2.6k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... Sorry, I did that as well, but I still get the same error. I edit my post now ...
written 14 months ago by dago2.6k
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Comment: C: gatk v4.14.0 does not recognize matematical operators
... I also posted this issue on the gatk github, sorry for the double posting ...
written 14 months ago by dago2.6k

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