Input only the gene expression matrix

kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

https://kharchenkolab.github.io/numbat/

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Input only the gene expression matrix #187

Closed Moey-git closed 1 month ago

Moey-git commented 1 month ago

Hi, TengGao@teng-gao, I am very interested in your research, but I have encountered some problems. I wonder if it is possible to run numbat with just the gene expression matrix and no allele file？I would like to know how numbat-exp in Figure 2d in your article is made.

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

teng-gao commented 1 month ago

Hi, for Fig 2d we only benchmarked CNV detection from pseudobulk using the haplotype-aware Hidden Markov model. I have a parameter in the internal function here that allows expression-only analysis. The overall Numbat workflow does not support expression-only mode.

Moey-git commented 1 month ago

Thank you for your prompt reply！