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navinlabcode / copykat

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About the mouse gene mm10 #22

Closed sgh212 closed 2 years ago

sgh212 commented 3 years ago

Hi,

Thank you for developing this method! Please add MM10? how to change the reference genome like mm10?

gaobio commented 3 years ago

Hi,

Thank you for developing this method! Please add MM10? how to change the reference genome like mm10?

Yes, I have being alway thinking of adding this compatibility. I doubted if it worth it because mouse genome seemed do not have many CNAs. Happy to test if you see CNAs are common in certain mouse samples ...

plenehan commented 3 years ago

Seconding this request. Would be great to enable this method for identification of aneuploid cells from mouse tumor scRNA-seq datasets. CNAs indeed may be less common across mouse cancer lines than human cancers, but there are models where this could be quite useful. Thanks for the nice and easy to use package!

gaobio commented 3 years ago

Seconding this request. Would be great to enable this method for identification of aneuploid cells from mouse tumor scRNA-seq datasets. CNAs indeed may be less common across mouse cancer lines than human cancers, but there are models where this could be quite useful. Thanks for the nice and easy to use package!

yep - started to work on it recently. There will be a tutorial to guide users to generate their own references for different species. Thanks for your patience.

LYZ2021 commented 2 years ago

Seconding this request. Would be great to enable this method for identification of aneuploid cells from mouse tumor scRNA-seq datasets. CNAs indeed may be less common across mouse cancer lines than human cancers, but there are models where this could be quite useful. Thanks for the nice and easy to use package!

yep - started to work on it recently. There will be a tutorial to guide users to generate their own references for different species. Thanks for your patience.

Thanks for the contribution to a great method like this! Waiting for a update on the mouse genome.

chatterjee89 commented 2 years ago

Seconding this request. Would be great to enable this method for identification of aneuploid cells from mouse tumor scRNA-seq datasets. CNAs indeed may be less common across mouse cancer lines than human cancers, but there are models where this could be quite useful. Thanks for the nice and easy to use package!

yep - started to work on it recently. There will be a tutorial to guide users to generate their own references for different species. Thanks for your patience.

Any update on this?

gaobio commented 2 years ago

Finally working on it now. Very sorry for the delay.

gaobio commented 2 years ago

@LYZ2021 @chatterjee89 @plenehan @sgh212 The mouse module is up now. Due to my limited tests on mouse scRNAseq data, this first version only output copy number results using gene names as coordinates, instead of genomic positions. All genes used in the calculated are labeled in the bottom of the heatmap.