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Dear prof. Zhang,
I used the IIIVmrMLM to analyis the epistasis loci, but there were an errors as follows:
"Epistasis analysis for yield begins"
Error in SetMatrixElements(x@address, as.double(j)…
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The current implementation of the global epistasis model doesn't guarantee monotonicity between the output of the initial linear layer and the final output. In my experience, the easiest way to guaran…
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cc @ValWood and @kimrutherford
Today I was curating a paper in which they show that:
* deletion of gene X causes an increase in protein A levels
* deletion of gene Y causes an equal / very simila…
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@caelanradford and @jbloom might find this helpful.
I just discovered `pylint`'s UML (unified model language) tool, `pyreverse`. You can call pyreverse from your command line on any python file an…
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- [ ] icons for all 20 canonical amino acids and protonation states
- [ ] coevolution
- [ ] salt bridge icon
- [ ] epistasis icon
- [ ] interaction network in protein
Inspiration
![image](h…
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Infinite log likelihood errors: It should never happen!
Add test case.
Exception in thread "main" java.lang.RuntimeException: Likelihood ratio is infinite! ID: 1:57158149_C/T,G-7:157931143_C/T
…
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Hello!
While running through the GPseer tutorial, I experienced a bug while running the following command with the raw pfcrt data:
`gpseer cross-validate pfcrt-raw-data.csv --spline_order 2 --s…
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`multidms==3.0` introduces a much easier interface for fitting collections of models in parallel. @Caleb-Carr and I have put together this issue to serve as an outline/plan for updating the notebooks …
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The idea is to make a specific case to predict how interactions change after the deletion of 1/2/multiple genes starting from the specific case of the polarity network, which would allow us to include…
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Ideally, would like to extend concept beyond just the host-microbe interaction, and allow for a bit more nuance e.g. you could input a single genome but see if linkage groups were interacting with eac…