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data2intelligence / SpaCET

Spatial Cellular Estimator for Tumors
GNU General Public License v3.0
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Differential expression (like in your paper) #24

Open Magisterh1 opened 8 months ago

Magisterh1 commented 8 months ago

Hi!

I really like your tool! I need to calculate differential expression between certain spots like you did in Figure 6c / 6d of your paper "Estimation of cell lineages in tumors from spatial transcriptomics data". Can you provide me with some code how to select/group spots and how to perform the DE?

Thank you!!

beibeiru commented 8 months ago

Hi, @Magisterh1 ,

Thank you for your interest in SpaCET.

Per your request, I developed a new functionality in our package. You can open up an interactive visualization panel by setting interactive=TRUE to browse all your results. Particularly, you can select and download the spots of interest.

SpaCET.visualize.spatialFeature(SpaCET_obj,interactive=TRUE)

After getting two groups of spots, you can use the shared code in the following link to perform DEA and GSEA. https://connecthkuhk-my.sharepoint.com/:f:/g/personal/bbru_connect_hku_hk/Ehqq12EU2oBHmPOTrgbjnNMBE016IsQDn9U7NlbH14RDfQ?e=X0XHhC

Please let me know if you have any further questions.

Best, Beibei