Valentine Svensson

In the STAR alignment, what proportion of reads are aligned to exons?

Hi everyone, Including log scaling of any quantitative scale in cellxgene would be immensely helpful. I think a lot of thing that are easy to make clear with custom plots...

My opinion would be to trust the user to know what they are looking at. I'm not aware of any plotting/visualization software that prevents using log scales because the user...

Hi, This issues relates to a couple of things I am interested in. Let me illustrate with a data set I have been working on. If you find some clusters,...

I would argue that Kallisto is "cheating" a bit by looking at expression of the equivalence classes :p, avoiding the ambiguous assignment issue. Just offering an opinion as a Salmon...

I think not doing the demultiplexing is better for practical issues. I have a dataset with 120 000 cells, and I don't think a file system can handle these. And...

Hm, you're right, it should be! Not sure why we missed that. Looking at simulations from null model, the FDR is calibrated: https://github.com/Teichlab/SpatialDE/blob/master/Analysis/Theory/Simulation%20from%20null%20model.ipynb . But the black bar might be...

If I understand correctly what you are asking, I think this is what we did with the 'bifurcation_statistics'. For each gene, we created one 'overlapping mixture of Gaussian processes' (OMGP)...

Hm for some reason that method (`m.calculate_bifurcation_statistics()`) doesn't seem to actually capture the output from the `bifurcation_statistics()` function. If you run the function instead, as in ``` diff_stats = bifurcation_statistics(m.fate_model,...

In theory you could pass the likelihood ratio (`D`) to a chi-square distribution. But it is unclear what the difference in degrees of freedom is between these models. In the...