User: ariel

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ariel110
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Posts by ariel

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Answer: A: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... I think for an experimentalist who wants to understand why use one of these packages over the other, or any at all, most of these explanations are rather vague. They may not have any idea what is meant by "different statistical model." This is what I would do: 1. briefly restate the purpose of the ...
written 7 months ago by ariel110
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Comment: C: What is the current state-of-the-art for differential abundance in microbiome pa
... I like that idea, but it would sacrifice the abundance information. I'm going to try linear regression on the log aundances and see what happens. The log distributions don't look "too" bad. ...
written 8 months ago by ariel110
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Comment: C: What is the current state-of-the-art for differential abundance in microbiome pa
... Thing is, we have a lot of important covariates, so Mann-Whitney or Kruskal-Wallace won't work :( ...
written 8 months ago by ariel110
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What is the current state-of-the-art for differential abundance in microbiome pathway analysis?
... I've seen other folks use DESeq2 for performing differential abundance analysis after pathway annotation with picrust2, piphillin, tax4fun, etc. However, when I look at my KO (KEGG Orthologs) abundances or mapped pathway abundances, they are definitely NOT ZINB (zero-inflated negative binomial) dis ...
microbiome deseq2 pathway analysis kegg written 8 months ago by ariel110
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Comment: C: NOOB education needed for microbiome functional analysis (specifically PICRUSt2)
... After reading more docs, it turns out the picrust2 ONLY uses the EC numbers and gets the pathways from the MetaCyt database. It gives me the KO numbers, but does not match them with KEGG pathways. ...
written 8 months ago by ariel110
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Comment: C: NOOB education needed for microbiome functional analysis (specifically PICRUSt2)
... Both, I think. Going from Taxa -> KO, am I ending up with all possible gene orthologs in that specific organism, or is it the orthologs represented across all the samples in the pool? Maybe that is the difference between "stratified" and "unstratified?" Then, is it just KO -> pathway, or is it ...
written 8 months ago by ariel110
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NOOB education needed for microbiome functional analysis (specifically PICRUSt2).
... I give picrust2 a list of 16s ASVs that map to biota at various taxanomic levels. Picrust2 creates a table of inferred per-sample abundances of KEGG genome orthologs (KO) and one of KEGG enzyme classifications (EC). The main output is a list of per-sample inferred pathway abundances that seems to ta ...
microbiome 16s picrust functional-analysis written 8 months ago by ariel110
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Comment: C: R package for Unifrac and Weighted Unifrac other than Phyloseq?
... Thanks @Jean-Karim. I'm trying to get away from using Phyloseq in general which is why I asked for an alternative. I've been switching over to working directly from tables as I find I have more control, write tidier code, and reduce the size of r sessions. ...
written 12 months ago by ariel110
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Comment: C: R package for Unifrac and Weighted Unifrac other than Phyloseq?
... You are kidding, right? ...
written 12 months ago by ariel110
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Answer: A: Normalization for microbiome 16s sequence analysis.
... @Carambakaracho -- thanks for checking back! In fact, I received no response here or on http://bioinformatics.stackexchange.com/. This surprised me because it seems like a very important question. Fortunately, I did get some valuable response at the QIIME2 forum that you might find interesting. ht ...
written 12 months ago by ariel110

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Scholar 12 months ago, created an answer that has been accepted. For A: Normalization for microbiome 16s sequence analysis.

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