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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
129 stars 44 forks source link

customized pathway database #97

Closed lindongdo closed 10 months ago

lindongdo commented 1 year ago

Dear developers, I was looking for a way to import customized pathway database (e..g, gmt file) for geneset visualization and gsea analysis. Do you have any suggestions? Also, the new version of cellxgene provides some cool functions for geneset visualization, will cellxgene vip be able to sync those geneset info with cellxgene as well?

Thanks! Dongdong

z5ouyang commented 10 months ago

Yes, you can download/prepare GMT files, and put them into the "gsea" folder, and run ./update.VIPInterface.sh, all those GMT files will be copied into the VIP and you will be able to see them in your next VIP lanuch.