For getting started, we recommend Scanpy’s reimplementation of Seurat’s [Satija15] clustering tutorial for 3K PBMCs from 10x Genomics, containing preprocessing, clustering and the identification of cell types via known marker genes.
For more possibilities on visualizing marker genes, see this plotting gallery.
You can extend this to multi-resolution analyses of whole animals, such as the Planaria PAGA example:
The PAGA method behind this is described in [Wolf19]. As a reference for simple pseudotime analyses, we provide the diffusion pseudotime analyses of [Haghverdi16] for two hematopoiesis datasets: The Paul DPT example [Paul15] and the Moignard DPT example [Moignard15].
Conversion: AnnData, SingleCellExperiment, and Seurat objects¶
See the Seurat to AnnData notebook for a tutorial on
Simulating single cells using literature-curated gene regulatory networks [Wittmann09].