songbird
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biocore
Vanilla regression methods for microbiome differential abundance analysis
So, installing Songbird via conda-forge into a fresh QIIME 2 2020.2 environment now _works_, at least insofar as getting Songbird installed. (Like, importing Songbird into python works, running `songbird multinomial...
Hi, I am using a Mac Catelina This is what I did when installing ``` conda create -n songbird_env python=3.6 numpy=1.15.4 scikit-bio=0.5.5 seaborn pandas=0.23.4 -c conda-forge source activate songbird_env conda...
Hello, I am trying to use songbird to analyze the redsea dataset from the tutorial but I am getting an error when calling tensorboard. The initial step (code below) works...
I am putting this comment here, but it also impacts the examples for mmvec (and maybe other programs). The 'red sea' example for songbird uses sampleid as an identifier for...
This has come up before, but I'm making it an issue here so it's officially written down somewhere. From discussion with @antgonza and many other people :) Relates to biocore/qurro#229.
Thanks for developing Songbird, it seems like it will be a useful tool. However, I’m trying to run it as a stand-alone program on our cluster here at Tulane and...
This is causing problems with the standalone songbird installation instructions. Easiest solution is just modifying this part of the README to specify the pandas version, ideal solution is modifying the...
Something I've been thinking about is that, to a pretty large degree, "using Songbird" boils down to choosing a formula. I know that the current README already links to the...
Sooner or later, this discussion will pop up. There will be some numerical issues when converting back and forth between alr and clr coordinates. In otherwords, you shouldn't need to...
Talked about this with @cameronmartino. Essentially, the red sea dataset used in the README is a really "nice" example of a model fitting -- this is great but can be...