mmvec
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biocore
Neural networks for microbe-metabolite interaction analysis
This comes from another discussion with @wasade. It could be useful to enable simple hypothesis tests for microbe-metabolite interactions. As shown in the CF study, we can perform a t-test...
There could be a command line option to set the max GPU memory allocation. By default tensorflow pre-allocates 100% of the GPU memory. If its not needed, then enabling the...
Version 1 is coming up in the next couple of weeks. We need the following resolved ASAP - [x] Rename rhapsody to mmvec (see [twitter post](https://twitter.com/biorxivpreprint/status/1162325887121002498) for why) - [x]...
The following needs to be included in the tutorials - [x] qiime2 import - [ ] GNPS links / download and unzip - [ ] Docker installation - [x] Heatmap...
There is a version1 branch on mmvec, but that is now a misnomer since the version1 release will be with Tensorflow. We will need to rename this branch to `pytorch`.
Hi, So here's a command run on a gpu node in an interactiove slurm srun session: ``` $ rhapsody mmvec \ --microbe-file A.biom \ --metabolite-file B.biom \ --min-feature-count 5 \...
Will include 3: 1. Rhapsody for CPU 2. Rhapsody for GPU 3. Rhapsody in Qiime2
Relevant to #75 One question is, how can one choose the right microbes? Right now the only way to do this is to select microbe by pointing and clicking through...
In the old version of mmvec, we stored histograms of the parameters - this has not been added into pytorch yet. I'm thinking this maybe a good time to refine...
Since we are going to be doing a refactor of the CLI anyways, it maybe worthwhile to think about what commands to have. Right now, we have ``` rhapsody mmvec...