Step-by-step guides to iSCanGuide.
Shows how to create a study and bring data into it: naming the study, sharing it, choosing a data type and source, uploading files, reviewing samples, filtering on quality, and saving the result.
20 stepsShows how to explore your data on the analysis page: creating views, choosing what each one shows, arranging them, filtering and syncing them, and saving your work.
14 stepsShows how to create an embedding: choosing what to build, selecting cells and features, setting normalization, standardization and integration, regressing unwanted genes, and choosing a visualization method.
11 stepsShows how to group cells by expression similarity: choosing an embedding and a method, setting the parameters, and using the clusters in the rest of the app.
7 stepsShows how to assign cell type labels to your cells: by hand, from enrichment results, or automatically with SingleR, CellTypist or Geneformer.
12 stepsShows how to compare two groups of cells to find the genes that separate them: defining the groups, choosing a method, reading the results table and volcano plot, and saving genes to a gene set.
13 stepsShows how to build and manage the gene sets used for enrichment, feature filtering and annotation, by uploading a file, pasting text, entering sets by hand, or taking them from the built-in database.
8 stepsShows how to test gene sets against your data, either scoring every cell or testing the genes from a differential expression result, and how to use the scores in a view.
8 stepsShows how to find ligand-receptor interactions between cell types: setting up the analysis, choosing a resource, and reading the results across the tabs.
13 stepsShows how to order cells along a developmental or transitional path: choosing between StaVia and Slingshot, setting the grouping and starting point, and viewing the result.
9 steps