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We should check that DESeq2 is run in a best possible default way.
For example:
> In version 1.16 (November 2016), the log2 fold change shrinkage is no longer default for the DESeq and nbinomWa…
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**Update:**
I found a way to pull the coefficients for the model. I still can't pull the correct coefficients using the method I originally asked about.
Method that works, in case it helps someo…
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By default sample estimate is used to estimate the covariance in Fisher discriminant such as LDA and QDA. However it could be useful to make the API a bit more general so that any estimator of covaria…
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Hi, #20 has offered two variants on the Ledoit-Wolf shrinkage estimator that are undocumented. I did some backtests and I believe that the single factor target may be better than the default constant …
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**Describe the bug**
Running the rna-seq pipeline throws an error.
[2020-08-07T093329.002444.snakemake.log](https://github.com/vanheeringen-lab/seq2science/files/5039975/2020-08-07T093329.002444.…
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I'm trying to understand how to fetch final model.
Y=theta(X)*alpha*T+f(w)
I think effect interval seems like giving the CI for coefficient alpha, but I'd like to get details of theta(X), for exampl…
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I have a single trajectory and a corresponding pdb file and I just want to try the tICA analysis on it. From msmb tICA help command I got the following inputs
-i INP, --inp INP Input dataset. T…