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VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
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User-defined pseudo-bulk samples? #30

Open borshago opened 3 years ago

borshago commented 3 years ago

Hi,

I have data with cells from various individuals representing two different groups, and I'm interested in comparing the same cell types between the groups. I would like to use the individuals as replicates when running DEXSeq for DTU. Is there an easy way to modify the existing code so that the pseudo-bulk samples correspond to all the cells of interest in the available individuals?

Best, Daniel

rj-patrick commented 3 years ago

Hi @borshago,

Thanks for the suggestion. I've made a modification to DUTest so that you can define a set of replicates for the input. When running DUTest, instead of defining population.1 and population.2, you can input a list (where each element in the list is a vector of cell IDs) through the parameters replicates.1 and replicates.2. I.e. the length of the list will correspond to the number of individuals in your data.

Let me know if you have any issues. I will try to add an example to the Vignette in the near future.

Cheers, Ralph