tinyi
commented
1 year ago Hi Chang,
We haven’t benchmarked extensively for ATAC deconvolution, but I do not see any reason why this cannot be generalized to ATAC - provided everything is at the count scale which should naturally follow multinomial distribution. We have tried to deconvolve enhancer RNAs measured by PRO-seq using scATAC-seq, and it worked well. The input should be formulated as count matrix over the peaks.
Best,
Tinyi
On Wed, Sep 14, 2022 at 11:01 PM Chang Kim @.***> wrote:
Hello,
I was wondering if this could potentially be used for scATAC-seq reference peaks to deconvolute bulk ATAC-seq expression? Specifically I was wondering the constraints on the input matrix for such a way to have it work? I'm assuming I need to convert the peaks into an integer matrix.
Best, Chang
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Hello,
I was wondering if this could potentially be used for scATAC-seq reference peaks to deconvolute bulk ATAC-seq expression? Specifically I was wondering the constraints on the input matrix for such a way to have it work? I'm assuming I need to convert the peaks into an integer matrix.
Best, Chang