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mandichen / copyVAE

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How to get Fig2a in the article #5

Open Mashuaiii opened 3 months ago

Mashuaiii commented 3 months ago

@mandichen Hi，mandichen

Good job and I am very interested in your research, but I have some questions.I used the sample data BM2_v0s0_n_200.h5ad and Macosko_cell_cycle_genes.txt to get the following result file, clone_0_breakpoints.npy, clone_0_profile.npy, clone_0_single_cell_profile.npy, copy.npy, I want to know if Fig2a in the article is generated through these result files, could you please provide relevant codes

I am looking forward to hearing from you and I would appreciate it very much. Best regards！

23ycjiang commented 3 months ago

Hello,Moey-git I have some questions about the DCIS1 dataset and I really need your help. In copyvae, only the data of RNA-SEQ are provided for CNV detection. Then the bulk DNA sequencing and whole-exome sequencing analysis methods served as ground truth when carrying out the index middle distance calculation of this method Where can I download reference? I only found the same scRNA data in the copykat paper mentioned in the article. Looking forward to your reply very much. Thank you very, very much. Your reply is important to me.

Mashuaiii commented 3 months ago

Hello,Moey-git I have some questions about the DCIS1 dataset and I really need your help. In copyvae, only the data of RNA-SEQ are provided for CNV detection. Then the bulk DNA sequencing and whole-exome sequencing analysis methods served as ground truth when carrying out the index middle distance calculation of this method Where can I download reference? I only found the same scRNA data in the copykat paper mentioned in the article. Looking forward to your reply very much. Thank you very, very much. Your reply is important to me.

Hello，23ycjiang I'm terribly sorry. I didn't know that either.

23ycjiang commented 3 months ago

Did you find the WES or WGS data paired with scRNA? I look forward to hearing from you.