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acycliq / pciSeq

A probabilistic cell typing algorithm for spatial transcriptomics.
MIT License
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gene-by-cell matrix #6

Closed rocketeer1998 closed 2 years ago

rocketeer1998 commented 2 years ago

Hi @acycliq , any recommendation about creating a gene-by-cell expression matrix without using scRNA-seq data? In other words, I want to assign each ISS spot to the corresponding cell where the value is the raw count number of each spot, which is different from the present expression matrix that stores the processed value.

The reason for it is that I want to do some scRNA-seq analysis, including dimension reduction, unsupervised clustering, differential expression, etc. But the result is not that good using present expression matrix.

acycliq commented 2 years ago

I image you have tried just looking at the segmentation, If a spots is inside the boundaries then assigned it otherwise it is on the background. But you dont need pciSeq for this.