BIRDMAn
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biocore
Bayesian Inferential Regression for Differential Microbiome Analysis
Below is an example of one of these error messages ``` Traceback (most recent call last): File "/home/centos/birdman/run_single_feature.py", line 110, in model.fit_model( File "/home/centos/miniconda3/envs/birdman/lib/python3.11/site-packages/birdman/model_base.py", line 173, in fit_model self.fit =...
We should have a summary function that mirrors the arviz summary object https://python.arviz.org/en/latest/api/generated/arviz.summary.html I'm not sure if this is directly applicable out of the box (since our objects are a...
Allows for users to specify fixed and random effects and creates Stan file + class
Dear @gibsramen and @mortonjt, I built a formula to look for the effects of two variables likely affecting tadpole gut microbiome: temperature (with 5 levels) and nitrate concentration (with three...
Dear all, I have been trying to compare my model with a null model and although all the cells seem to run perfectly (no error messages) my kernel always dies...
I installed `v0.1.0` via the following: ``` conda install -c conda-forge biom-format patsy xarray arviz cmdstanpy pip install birdman ``` When I try to run a negative binomial model, I...
I'm following the tutorial here: https://birdman.readthedocs.io/en/stable/default_model_example.html With other software like ALDEx2 and edgeR you can specify a cutoff using FDR. I understand that working in a bayesian framework is different...
Eventually, it would be nice if there was support for [Variational Inference](https://cmdstanpy.readthedocs.io/en/v1.0.1/examples/Variational%20Inference.html). It can be significantly faster than MCMC, with the caveat that the posterior estimates aren't accurate.