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I have some .fna files after quality control. Now i want to use these files to run through microbiome workflow in R, but i don't know how to read these files in R and process these. Can dada2 read the…
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Hi all,
I am analysing 16S MiSeq data from 3 separate runs for the same project. The 3rd MiSeq run had a higher sequencing depth. Partly for this reason, I observe a significant batch effect, where…
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I imagine this would work best as a separate tutorial (analogous to the moving pictures one), but using Qurro standalone instead of through QIIME 2. Depending on where we get the data from, we could c…
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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/waldronlab/lefser
Confirm the following by editin…
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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/Guan06/mina
Confirm the following by editing each…
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**Submitting author:** @grabear (Robert Gilmore)
**Repository:** https://github.com/vallenderlab/MicrobiomeR
**Version:** 0.6.0
**Editor:** @lpantano
**Reviewer:** @CosteaPaul
**Archive:** 10.5281/ze…
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Somewhat of an edge case, but following host read removal some of our samples, e.g. blanks, can wind up with no reads in the output fastq file. It looks like this causes an unhandled exception with th…
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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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Hi,
I am following the microbiome workflow on
https://bioconductor.org/help/course-materials/2017/BioC2017/Day1/Workshops/Microbiome/MicrobiomeWorkflowII.html
It runs fine up to the command fil…
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