Tools for scRNAseq

Question

[wenbinm]

Hi there,

Any suggestions on R or python packages to analyze tumor scRNAseq data, if I want to distinguish malignant cells from normal cells?

Thank you!

[alireza.khodadadi.j]

single cell RNA sequencing

[GenoMax]

Please do not post this in every single cell RNA thread. You have already created a tools post for your software which is the appropriate way of announcing a new tool.

[Biological information research group o…]

Seurat,Linnorm,Dimm-SC，It can all be done, and I'm glad it helps

Answer 1

[GenoMax]

@Sean Davis has a comprehensive list of programs related to all things single cell here.

[wenbinm]

Thank you for your response! I also saw that list. Do you know some specific tools? I found several papers first estimated CNV based on transcription data (cells with many CNVs are tumor cells), but they didn't tell which tool they were using (maybe everybody writes their own code and there is no universal tool?)

Answer 2

[wenbinm]

I finally discover that I can do this by first inferring CNV (using infercnv for example). Malignant cells have CNV while non-malignant cells don't. Then they can be distinguished.

Answer 3

[predeus]

There's a good list here: https://www.scrna-tools.org/table