User: ariel

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ariel40
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1 week, 4 days ago
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3 years, 5 months ago
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a****@arielbalter.com

Posts by ariel

<prev • 13 results • page 1 of 2 • next >
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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 15 days ago by ariel40
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Comment: C: R package for Unifrac and Weighted Unifrac other than Phyloseq?
... You are kidding, right? ...
written 16 days ago by ariel40
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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 18 days ago by ariel40
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Answer: A: How to normalize my results after DESeq2
... As @swbarnes2 said, it sounds very much like you are using the right tool for the wrong job. DESeq isn't so much a package as an implementation of an algorithm for performing DE on raw RNA-Seq counts, where an important step in the algorithm is normalizing the counts. This process uses a special al ...
written 20 days ago by ariel40
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R package for Unifrac and Weighted Unifrac other than Phyloseq?
... I've been googling, and I can't find an R package that calculates weighted and unweighted unifrac distances other than phyloseq. I'm doing all of my other analysis by hand from tables, so if possible I'd rather not have to convert to phyloseq objects just for this part of the analysis. ...
R written 20 days ago by ariel40
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Comment: C: simple explanation needed
... Or, if you can't explain it simply, then you don't really understand it. Sounds cliche, but I believe it. ...
written 27 days ago by ariel40
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Normalization for microbiome 16s sequence analysis.
... The way I understand things, normalization (such as in DeSeq2, EdgeR, etc.) serves two purposes: 1) Model the "real" abundance in the original samples from the read counts, 2) Make the abundance distributions conform to the needs of statistical analysis by removing heteroskedasticity, dependence, di ...
microbiome 16s miseq rna-seq written 29 days ago by ariel40
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Comment: C: Should all microbiome analysis be done after normalization?
... It's done now. Sorry :) ...
written 4 weeks ago by ariel40
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A modern way to perform the analysis that LEfSe does?
... Given the developments and increased access to machine learning algorithms such as LDA that have happened since [LEfSe][1] was developed, is there now a way to perform the same analysis with standard tools? The LEfSe code base is in pretty primitive python 2.7 and is not even organized as a package ...
microbiome effect size lefse lda written 11 weeks ago by ariel40
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Comment: A: How to integrate and visualize RNASeq / Proteomics data for metabolomics pathway
... I'm just starting on a similar project, and I have no idea either (never done metabolomics). If I figure some stuff out, I'll get back to you :) ...
written 3 months ago by ariel40

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Scholar 18 days ago, created an answer that has been accepted. For A: Normalization for microbiome 16s sequence analysis.

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