Totem

Description

Totem is a tool designed to facilitate the inference of tree-shaped trajectories from single-cell RNA-seq data. The key idea is to generate a large number of clustering results, rank them, and examine the resulting top-ranked clustering results. The probability of finding an optimal clustering increases when different clusterings are considered. Totem uses the Slingshot method to smoothen the lineages of the trajectory network. In addition, the cell connectivity measure derived from the cluster connectivity of Minimum Spanning Trees (MSTs) of the clustering results can be used to aid the trajectory optimization.

Code

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Topics

People

• Johannes Smolander maintainer author
• Laura L Elo author
• Sini Junttila author