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Hello,
I am trying to analyse differential abundances of bacterial taxa in subways. Using fitFeatureModel(). First I subset the MRexperiment object, keeping three levels of the factor "surface_type":…
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Dear Joey,
Thank you for developing phyloseq. I have been using phyloseq and find it extremely useful. I was drawn to using phyloseq because of your ‘Waste not, Want not’ paper, in particular the use…
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I am starting down the rabbit hole of figuring out which proteins are indicative of mass mortality events. [Here](https://github.com/RobertsLab/project-pacific.oyster-larvae/blob/master/DDA_2016/Qspec…
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Please consider a new term for hamartomatous proliferation containing malformed hair follicles in various stages of development .
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Hello,
I am trying to understand what the values are that are being reported in logFC after using fitFeatureModel. My code is below.
I have a metagenomeSeq object called Park_ShenCat that looks like…
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Hi Chris,
I have generated the Cluster_scgs.freq file (file size 4109754) and when I tried the variant_filter.py script I got this error, do you have an idea of what is going on? N is null?
Thanks…
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Dear Aaron,
In addition to an issue with binning, I am also having a problem regarding the plotFoldEnrichment function. I have attached both the code and associated plot for both counts and combina…
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Hi Joey, just a quick question - you recommend DESeq2 for differential abundance analysis when using phyloseq. I was wondering if you had considered the ALDEx2 R package, and if you had chosen not to …
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Hello,
When I am running DAS_TOOL. I have met some troubles. First, it tells me that "cannot stat '_proteins.faa.scg': No such file or directory". But I have installed diamond and Prodigal. Ar…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/MarioniLab/cydar
Confirm the following by editing…