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SCA-IRCM / SingleCellSignalR_v1

R package
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Questions regarding Seurat and SingleCellSignalR integration #5

Closed singcell closed 4 years ago

singcell commented 4 years ago

I am using SingleCellSignalR with Seurat tool as directed in Supplementary Box 2 of your publication. In the box 2 you have shown steps until visualization. Next I wanted to perform cell classification using cell_classifier function. However, I am not sure how I can integrate cell_classifier with the Seurat ouptput i.e "data = data.frame(pbmc[["RNA"]]@ data) ". DO I need to run clustering(data = data,n = 10, method = "simlr") after retrieving the results of the preprocessing from the Seurat object followed by Cell classification and Cluster analysis.

Thank you

SCA-IRCM commented 4 years ago

Hello, You can use the visualization function (see the User's Guide: https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/UsersGuide.html for more details). You can also use the cell_classifier function with the Seurat output counts data frame, see the details of this function for proper use. Thank you for using SingleCellSignalR.

SCA

singcell commented 4 years ago

@SCA-IRCM Thank you for your reply.