Question: Tools for scRNAseq
1
gravatar for wenbinm
2.0 years ago by
wenbinm20
USA
wenbinm20 wrote:

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!

rna-seq R genome • 789 views
ADD COMMENTlink modified 9 months ago • written 2.0 years ago by wenbinm20

single cell RNA sequencing

ADD REPLYlink modified 11 months ago • written 11 months ago by alireza.khodadadi.j60

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.

ADD REPLYlink written 11 months ago by genomax87k

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

ADD REPLYlink written 10 months ago by Biological information research group of Harbin medical university daqing campus10
1
gravatar for genomax
2.0 years ago by
genomax87k
United States
genomax87k wrote:

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

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by genomax87k

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?)

ADD REPLYlink written 2.0 years ago by wenbinm20
0
gravatar for wenbinm
9 months ago by
wenbinm20
USA
wenbinm20 wrote:

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.

ADD COMMENTlink written 9 months ago by wenbinm20
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