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Hi there,
I am currently dealing with a dataset of 16S OTUs from sediment of two Antarctic cruises. I notice that in some of the phyloseq tutorials, the following is used:
```
dds1 = phyloseq_to_des…
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I've drafted the following Slack message to send to our curators. @tosfos shall I send it now or do you want me to wait, and is there anything you want me to change or add?
@channel I’ve just made …
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Hi,
I am running Evaluate_diversity.sh but I am not sure about -d . Here is my reads information. Please let me know which number should I give for -d here.
In logfile.txt it is showing "Number of b…
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Hi,
I read your article about MetaDEGalaxy and found it very interesting. I was looking at the non-overlap paired end 16S workflow, and I would like some more details about it. Specifically, for …
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Hi, I am not sure which value I need to give here to configure pipeline..Please suggest...
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A conda environment named MetONTIIME_env is created, where seqtk, porechop, pycoQC, Nano…
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Hi,
I want to investigate the relative abundance of 5 genera, over 5 time points.
I've adopted the dada2 tutorial to analyze my own data, and have generated the seqtab.nochim (5 rows, 3587 cols) …
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Hi Dr. Love,
I am trying to do a differential abundance analysis with microbiome sequencing data suing DESeq2 package, but I keep getting errors after trying different approaches within the package…
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**Submitting author:** @grabear (Robert Gilmore)
**Repository:** https://github.com/vallenderlab/MicrobiomeR
**Version:** 0.5.1
**Editor:** @lpantano
**Reviewers:** @CosteaPaul
**Author instruction…
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Hi!
does phyloseq have a function that can summarize by taxonomic rank, like QIIME (http://qiime.org/scripts/summarize_taxa.html)?
I didn’t find anything, so I made my own functions, see below. (I y…
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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/mikelove/fishpond
Confirm the following by editin…