Christoph Hafemeister

I don't know what is causing this. Could you share (a subset of) the data and the exact commands that trigger that error?

Hi, currently there is no such parameter in the model, but it is an interesting concept that would be useful. I have to think about how we could implement this...

I have not seen this error before. Can you share the data and the exact steps that led to this problem? In the meantime, make sure to install the latest...

I'd be more than happy to have a look. If you want to share the data privately, use [email protected]

@ahmedmahfouz Thanks for sharing the data. It turns out that there is a 'cell' with zero counts that is causing the problem. After loading the raw data, I recommend plotting...

Thank you for reporting this. Yes, the example is broken - I will fix that. It should be ``` vst_out

The `correct` replaces the observed values of the independent variables (by default this is the log10 of the sum of all UMI counts in a cell - a proxy for...

Hi, When you run sctransform normalization you are standardizing the expression of each gene in each cell relative to all the other cells in the input matrix. That means that...

I agree with mtmorgan. loomR shouldn't make any assumptions on whether rows are genes or cells. but it should make sure that a matrix in a loom file is in...

Thanks for the explanation. However, I was just trying to validate that behavior using the .sim function with some toy parameters, but could not reproduce the DP density curves. [Crowell...