Cell Type Atlas and Lineage Tree of A Whole Complex Animal by Single-Cell Transcriptomics
The following notebooks provide the analyses based on partition-based graph abstraction (PAGA) (Wolf et al., 2017):
- planaria: inferring the lineage tree from the topology of the Planarian cell atlas
- preprocessing: same as planaria, but including all preprocessing steps
- epidermal-lineage: zooming into the pseudotime-reconstruction of the epidermal lineage
- subsampling: robustness of the tree under subsampling
- wildtype: robustness when using only wild-type samples
- vary-neighbors: robustness under variation of the number of neighbors in the single-cell graph
PlanariaVelocytoAnalysis provides the analysis using the velocyto.py package (Gioele La Manno et. al., 2017).
run_monocle2 reproduces the analysis using Monocle 2 (Qiu et al., 2017).