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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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Can someone (@PratikDJagtap) point me to the Galaxy-P proteogenomic workflow into which I should integrate my Omicron tools, e.g. CustomProDB and PSM2SAM? I checked the "Published workflows" section o…
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Hello,
As a school project, I am developing a Qiime User Interface in JAVA for Windows using SSH to access a virtualbox and run the scripts for Qiime. This is currently for personal (educational) …
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Hi I was wondering if we could store the number of sequences we read in and number of which were filtered. This way we can say that we filtered X% of sequences using the abovementioned function.
My…
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I am unsure if this is the most appropriate place to post this issue. I realize this may be more of a comment on the paper in question than DADA2, however I am specifically interested in the use of DA…
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I'd like to start a discussion on how to implement management of growth media. I can think of two approaches:
1. Add a new method to cobra.Model that takes either a dictionary or a json file with the …
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Hi all,
In the [tutorial](http://benjjneb.github.io/dada2/tutorial.html) you input taxa and seqtab.nochim to phyloseq without prior normalization/subsampling. Does that mean that we don't need to nor…
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"Bioconductor (http://www.bioconductor.org/) is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. It is based prima…
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I am using phyloseq-DESeq2 to normalize my sequencing data with the negative binomial method as in "Waste not, Want not." I have a large number of very low abundance OTUs which I would like to remove.…
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Hi Team Dada,
Is there a best-practices for running dada2 in parallel? I know that its one of the theoretical selling points but I am not sure of the best way to make use of it. In the tutorial, for …