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I've been going through the phyloseq tutorials, trying to implement the negative binomial variance stabilization by way of DESeq, (as in the 'Waste not, want not' paper) and I'm running into a bit of …
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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 …
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It is common with Illumina data to have paired-end reads. Sometimes overlapping, sometimes not, sometimes meant to overlap but sequence quality bad, reads shorter than planned, etc.
For the time bein…
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# Shun-Yi Jheng
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1. Department of Computer Science, National Chiao Tung University
2. OpenHouse, National Chiao Tung University
3. Information Technology Service Center, National Chiao…
fkztw updated
8 years ago
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I wanted to test drive the phyloseq -> DESeq2 capability, and I was following the instructions you set. However, with the changes in QIIME and their data repository of late, I can't seem to call:
m…
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Hi Joey,
hope this does not sound inane but was wondering if you'd consider an ordination plot feature that would have contours around points? Say each point is a individual or site that you sample …
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- ~~Change blurb at the top to~~
> Auburn University has developed into one of the largest universities in the South, while remaining in the forefront of higher education. Our students can choose fr…
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Hi,
I want to plot and run stats on a handful of OTUs only. I tried to use subset_taxa but this function only works for taxonomic levels, not OTU IDs. I checked the issue tracker and it seems that pr…
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Hi @joey711,
In response to #517 I have a suggestion on how to handle the OTU merging when merging across something large like an entire Taxonomy class. If we add the taxonomy data to the OTUtable, w…
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Hi,
## not exactly an issue but request fro help
I am unable to get a output file which can be used by Tax4Fun post Dada2 processing. I tried the otu_table and write_biom options to get a table cont…