Reference data for J20 Hippocampus Slide-seq analysis

dmcable / spacexr

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

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Reference data for J20 Hippocampus Slide-seq analysis #188

Open Vivianstats opened 5 months ago

Vivianstats commented 5 months ago

Dear Dylan,

Is the reference scRNA-seq data used in the J20 Hippocampus Slide-seq analysis available in this repository?

According to the code (https://github.com/dmcable/spacexr/blob/master/AnalysisCSIDE/j20/run_RCTD_j20_21.R), the name of the object is scRefSubsampled1000.RDS.

I was able to find reference_hypothalamus.rds in SingleCellPortal, but the cell type names in this object are different from those in the C-SIDE paper.

You advice is greatly appreciated!

Vivianstats commented 5 months ago

Just realizing that I should look for reference_hippocampus.rds (according to the readme file), but it's not available in SingleCellPortal.