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Hi,
I'm looking for study rhizosphere microbiote (fungi and bacteria) in R. I have two independent sequencing data (bacteria & fungi) and I would like to perform co-occurence analysis. I use phylo…
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Hello Metacoder devs,
It must be pretty straight forward but I'm having a hard time trying to plot relative abundance of the taxa in the whole dataset instead of OTU count as node_size in the heat …
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The types are:
metabolite table, gene table, otu table, pathway table, function table, ortholog table, taxon table
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I often convert my phyloseq object into a "tidy" data frame for data manipulation and visualization rather than using `phyloseq`'s built-in functions. The `psmelt` function is slow enough on medium to…
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Hi All,
I'm currently an undergraduate student at the University of Illinois at Chicago working with 16S rRNA data. I have noticed only two taxonomic ranks are present in my tax_table. Any ideas on…
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It would be cool to be able have a function to produce tables like this from `taxmap` objects for use in Rmarkdown documents and publications:
 indi…
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Hi,
I am getting a strange error message, when I try to run SpiecEasi:
`spiec.easi(phylo, method='mb', lambda.min.ratio=1e-2, nlambda=20, pulsar.params=list(rep.num=50))`
`Applying data transfor…
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Possibly add this to validate_demultiplexed_fasta.py (and perhaps change this name to validate_data_files or something more generic as it's doing a bit more than checking fasta sequences already):
A …