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It would be nice to be able to operate on bioms and metadata files that are in memory, rather than just reading from a file
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I'd like to add this to my github.com/jolespin/veba software package under the mapping module. Currently, I can only add packages from conda because the environments are so complex and there are many …
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Hi,
This should be a simple fix. When I try running the following in R:
system('vsearch --usearch_global 16s_13_5_precalculated.tab --db 97_otus.fasta --matched 16s_13_5_precalculated.tab --id 0.…
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Hello,
I am trying to install sourcetracker in a cluster computer and I am getting an error after I test if my installation was successful.
What I did:
> conda create -n sourcetracker2 -c b…
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It would be very useful to have some sort of abstraction above a whole dimension (collection of all regions). Which then enables the usage of things like #17 and the possibility to set blocks.
This…
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Looking at Visumap, the majority of those algorithms are found in scikit-learn or scikit-bio, namely
**Ordination**
- [SMACOF](https://github.com/scikit-learn/scikit-learn/blob/master/sklearn/manifol…
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Hi, I've never left a comment on GitHub before so I hope I'm doing this properly.
I'm running SourceTracker2 on a MacBook. I've previously installed SourceTracker2 into a dedicated virtual environm…
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Would be great to have the loadings associated with each OTU from a PCoA to better explore the taxonomic differences between samples/treatments. This can also be done by comparing OTU abundances with…
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Hi Joey
I have been using phyloseq a lot on many projects and find it very useful.
The sample data slot is really useful for analysing relationships between the microbiome and sample metadata, and …
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Dear Joey,
I am trying to make some ordination plots on my data, but I always encounter errors when I use `type = "samples"` using plot_ordination.
`> mydata`
`phyloseq-class experiment-level object…