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JEFworks-Lab / MERINGUE

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
https://jef.works/MERINGUE
GNU General Public License v3.0
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correlation between genes #21

Open JihyunKiminGithub opened 6 months ago

JihyunKiminGithub commented 6 months ago

Dear author, Thank you for providing these fantastic tools.

I am currently seeking assistance with utilizing the tool to calculate the correlation between genes using my VIsium data. It appears that the 'spatialCrossCorMatrix' function is capable of returning correlation coefficients. However, I am unsure about how to obtain p-values for the test at this particular stage.

Your guidance on this matter would be greatly appreciated.

Thank you, Jihyun.

JEFworks commented 6 months ago

Dear Jihyun,

Thanks for reaching out. There is a spatialCrossCorTest function available that will use permutation testing to provide p-values.

Here is a tutorial with more examples for your reference: https://jef.works/MERINGUE/simulation

Best, Jean