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As the title says, the model `SCVI` by default uses a normal VAE, conditioning on the batch label needs to be explicitly enforced by passing `encode_covariates=True` ( 3713894 changed the default beha…
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In an IRT context Andrich and Luo (2003; Journal of Applied Measurement, 4(3), 205-221) suggest to reduce the number of threshold parameter by assuming the thresholds are given by a fourth order polyn…
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Dear Cécile and Viviane,
I noticed a surprising result with my model. The formula I used for the linear mixed model is something like Y~age+X+age*X, where X is a grouping variable with values 1, 2,…
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Dear Cecile and Viviane
I am in the process of describing latent trajectories I have identified, and have a huge sample of predictors to consider. To reduce the number of predictor variables in the…
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## Documentation
- [x] create a doc folder to store all documentation-related files
- [x] ReadMe: add text introduction to the dataset
- [x] ReadMe: Add plots showing example images from the datase…
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I just came across an article that informed me that there was a concept of _Double ML_, where the unfamiliar portion involves Causal Inference. [Medium article here](https://towardsdatascience.com/do…
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We are currently working with Seurat v5 and encountering a notable discrepancy in the output size between DESeq2 and MAST when performing differential expression (DE) analysis. Our workflow involves:
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I have created a hlme model with lung function as a function of age, and selected the model with 4 classess.
```
m4
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Dear Seurat Team,
I am contacting you in regards to a question about how to use your _FindMarkers_ function to run MAST with a random effect added for subject. I have a single cell RNAseq dataset w…
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Hi,
I've found questions posted previously that are similar to my question but don't provide the full picture that is specific to the approach I'm using, so I'm asking here to make sure my approac…