Adding Datasets

How to add single-cell datasets.


To add single-cell datasets:

  • click Dataset Management > Import
  • drag and drop files to upload
  • provide a sample name for associated files
  • when done, click Import Datasets

Cell Ranger

R Objects

Seurat object specifics:

  • Idents(scdata):
    • used as clusters
  • levels(Idents(scdata)):
    • used as cluster annotation
  • scdata$sample or scdata$orig.ident:
    • used as sample identity
    • treated as integrated if > 1 unique values
  • umap or tSNE reduction:
    • used for scatterplots
  • harmony or PCA reduction:
    • used as corrected reduction for integrated datasets
  • var.features slot:
    • used as highly variable genes

Edit this page on GitHub