Michael McLaren

First, pinpoint when the names get changed. Check that the row names of the `taxa` and `ab` objects are the original QIIME2 names, as expected. ```r head(rownames(taxa)) head(rownames(ab)) ``` If...

Have you already looked at the data importing tutorial https://joey711.github.io/phyloseq/import-data.html? It explains how the matrixes should be before you call the `otu_table()` and `tax_table()` functions. You want the rownames of...

Sorry about the delayed reply; here are some hopefully useful thoughts. About the tree labels: The taxa/otu names in OTU, TAX, and TREE need match, when you combine them with...

My motivation for asking is that I'm making tibble ("tbl_df") methods for otu_table, tax_table, and sample_data that can handle the taxa and sample names being a data frame column rather...

@joey711 Sorry, I should have posted a code example to be clearer about what I was asking. I'm asking about going in the other direction---creating a `taxonomyTable` from a `data.frame`,...

@mr2raccoon You should be able to simply convert your data frames to matrixes first, with `as(df, "matrix")`, and then supply it to the phyloseq functions.

Thanks for looking into this @bryandmartin. I think I might be asking for something simpler than what you're thinking - I just want to be able to add offset terms...

It seems that the creation of developer tokens is currently disabled. Is that the only way to fix this still, besides disabling 2FA?

Another option to get around this issue without requiring a developer key seems to be to disable 2FA, login to geeknote, and then allow geeknote as an "Application" in your...

Hi @colinbrislawn, thanks for your interest and bringing this up again. I want to get the next major release out in the next few weeks and then will consider a...