Cell marker selection - Githubissues

CompEpigen / digital_sorter

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Cell marker selection #12

Open taiwaness opened 3 years ago

taiwaness commented 3 years ago

@chiehyujessie

Well known markers:

Cell Type	Markers
T cells (CD4+)	PTPRC, CD3D, CD4
T cells (CD8+)	PTPRC, CD3D, CD8A, CD8B
B cells	PTPRC, CD79A
NK cell	PTPRC, NKG7
Myeloid cells	PTPRC, LYZ
Endothelial	PLVAP
Fibroblast	ACTA2
Epithelial	EPCAM, KRT8

taiwaness commented 2 years ago

[ ] tumor vs. normal markers
[ ] our own dataset for showing maker expression

chiehyujessie commented 2 years ago

SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates (publication in 2020/06) https://pubmed.ncbi.nlm.nih.gov/32053146/ https://www.cellsurfer.net/surfacegenie Shiny app -> https://gundrylab.shinyapps.io/surfacegenie/

[ ] extract its surface prediction consensus (SPC) score to update our surface marker list
[ ] use GenieScore to order the results of marker selection instead of p-value
[ ] use the shiny app for marker selection (use small dataset to test first)