songbird
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biocore
Vanilla regression methods for microbiome differential abundance analysis
As far as I'm aware, these values are only computed using the `summarize-paired` QIIME 2 visualizer. It'd be ideal to support this for standalone Songbird, if possible (from going over...
We will want to have a more explicit definition of this at some point The formula was inspired by the pseudo R2 http://www3.stat.sinica.edu.tw/statistica/oldpdf/a16n39.pdf It'll be great to have the pseudo...
As I understand it, either of these will take a decent amount of work (from talking with @gwarmstrong last week it sounds like moving to TF 2 would be less...
Hey! I have two questions- 1. I have a biom file of microbial KEGG pathways for 100 host samples which are phylogenetically related. I was wondering if I can account...
It should be possible to retrieve the input strings for the `--p-formula` option for each regression model from the qiime2 providence. Would be super useful if these formulas could be...
Hi Jamie, Unless I am misunderstanding something, I think there might be an issue with the QIIME2 Songbird plugin regarding making the regression biplot. When I use your RedSea tutorial...
Would be great if we could handle null distribution for differentials and carve something that looks like a p-value
should we flag new users about problems with possible colinearity issues if their metadata categories are too similar (e.g. including a continuous value of BMI and a quartile category of...
It looks like the code for `_summarize()` assumes that both stats inputs have the same summary interval: https://github.com/biocore/songbird/blob/2c4cf016ba8689b48fff6ee7eb5231068da76b55/songbird/q2/_summary.py#L57-L60 As far as I'm aware, this isn't documented in the user-facing API...
Scalable poisson regression specifically tailored for categorical data