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interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
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DEG in VIP get different list of genes from FindMarkers function #37

Closed FADHLyemen closed 3 years ago

FADHLyemen commented 3 years ago

When I choose Welch's t-test(diffxpy) from VIP DEG, I got different list of genes when I run the below line in R:

 FindMarkers(pima_scrna, ident.1 = "DKD", ident.2 = "LD",group.by='sampletype', min.pct = 0.5,
                               test.use='t')

the logfc from VIP looks weird something like 1071.22 which is very big.

z5ouyang commented 3 years ago

Please refer to https://github.com/theislab/diffxpy thanks

FADHLyemen commented 3 years ago

I am not talking about diffxpy. I am talking about Welch's t test.