search

JCVenterInstitute / NSForest

A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing
MIT License
53 stars 20 forks source link

Use features identified by NS Forest in Seurat #8

Closed SHADJIA closed 1 month ago

SHADJIA commented 2 years ago

Hello,

I tried your code to delineate the minimum marker genes to characterize subsets of Treg cells. Generally, I work with Seurat package to analyse my singlecell projects. I would like to generate a UMAP plot by using genes identified with NS Forest (2.0 and 1.3). For that, I did a subset of the initial SeuratObject by specifiying the identified genes as features. Then, I performed "FindNeighbors", "FindClusters" and "RunUMAP". Typically, I find the same plot between the one with 2000 genes and the one with 50 genes. Have you ever tried to combine Seurat and your tool, rather than Scanpy?

Thank you in advance

yunzhang813 commented 1 month ago

Thanks of the ticket. Code refactored in v4.0.