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Hi, I apologize in advance if this is answered somewhere in the documentation that I haven't been able to find yet. How does estimate_richness deal with uneven sequencing depth? I was under the impres…
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Hi all,
I am running an analysis on Naopore amplicon data (without primer processing, since it is a multiplex study, which I want to trim and treat further downstream) but get the following error …
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Possible regression found:
when using vegan::rarify (v2.6-4) on an phyloiseq@otu-table object , it returns 'Error in as(x, "matrix")[i, j, drop = FALSE] :
(subscript) logical subscript too long…
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Hi
Many thanks again for the package.
I have already ran my alpha diversity analysis (after rarefaction to the first quartile) and would like to add more info from the functional diversity side of…
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Remember to do the final diagnostics (which you should have done to start with!)
- Plot sequence abundance vs richness. Whatever the outcome, you may have to explain it if there is a relationship. …
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Dear all,
I recently performed an analysis on my dataset:
- investigating soil bacterial communities (ASVs obtained via 16S Illumina-sequencing)
- two different vegetation types [Sedum (5 habit…
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I would be nice if rarefaction curves could be plotted with phyloseq
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Hi!
I apologize if the question has already been asked, perhaps in other terms...
The Authors states in their recent papers that "normalization method introduced in ANCOM-BC performs well",
But …
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copied from https://github.com/umb-oconnorgroup/plasmodium_snp_call_pipeline_wdl/issues/3
Add support for subsampling BAM files to determine if sequencing was performed sufficiently. More specifica…