Comparing groups of single cells
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Hi Yuanhua,
I want to perform differential splicing of different groups of single cells. Could you provide an example for groups as I did not find this in the manual.
Thanks
Hi,
Thanks for using BRIE to detect differential splicing between groups of single cells. Here is a formal suggestion on it:
"For detecting differential splicing between two cell groups, there are two options. The first option is pooling reads from all cells within a group, and quantify splicing as one ensemble sample, which can be simply done by listing all cells with comma separation in brie. Then brie-diff can detect the differential splicing events between any pair of ensemble samples. This option assumes a homogeneous splicing level across the group, and it requires an additional splicing quantification besides the routine cell-level quantifications. Alternatively, one may use BRIE to quantify splicing in individual cells in each group, and then use a standard hypothesis test, e.g. Wilcoxon, to detect significant changes in the point estimates between two cell populations. This procedure requires however a sufficient number of cells in each population to achieve statistical power, and it ignores the uncertainty in the estimate. The original paper used the first option; we are currently developing a hierarchical model to perform differential splicing analyses while considering the uncertainty and heterogeneity within cluster."
In practice, I would recommend the second option if you have suffcient cells after filtering out the cells with 95% confidence interval > 0.3 (for axample) for each splicing event.
Cheers,
Yuanhua
@huangyh09 do you have a working prototype for the 2nd option? I'd very interested in trying it out
@huangyh09 @aopisco Have you got the working prototype ?thanks