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wuaipinglab / ImmuCC

Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
http://218.4.234.74:3200/immune/
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Applying ImmuCC on RNA-seq data #2

Open Ranemix opened 6 years ago

Ranemix commented 6 years ago

Hi, I have read your article “Inference of immune cell composition on the expression profiles of mouse tissue” and I am looking forward to using ImmuCC in my model, but I have RNA-seq data. Here in the code tab, I have found a file called “RNAseq_pipeline.sh” (https://github.com/chenziyi/ImmuCC/blob/master/webserver/RNASeq_pipeline.sh). Does it mean that it is possible to use ImmuCC with RNA-seq data? Has it been tested or validated somehow? I would really appreciate any thoughts about this issue.

leiendeckerlu commented 6 years ago

I'm also interested in applying your deconvolution function to RNAseq data....

chenziyi commented 6 years ago

Thanks for you interesting for our work. The scripts called “RNAseq_pipeline.sh” was used for RNA-Seq data preprocession. You can submit your sequencing data directly to a testing web server developed by us (http://wap-lab.org:3200/immune/). However, you can also give us your suggestions and recommendations for it since the web server is still a testing version.

Mirsus commented 5 years ago

Hello!

I would also like to use ImmuCC with my RNAseq data. I do have some suggestions and questions to make: 1) I would suggest you inform how the data should be entered (file extension) and also briefly explain how the scripts should be used. 2) Is it OK if I use it with my differentially expressed genes? or should I only use it with my data after the preprocessing you suggest?

Thanks and very nice work!