Cell Type Atlas and Lineage Tree of A Whole Complex Animal by Single-Cell Transcriptomics

PAGA

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

Velocyto

PlanariaVelocytoAnalysis provides the analysis using the velocyto.py package (Gioele La Manno et. al., 2017).

Monocle

run_monocle2 reproduces the analysis using Monocle 2 (Qiu et al., 2017).