A user-friendly tool for inferring tree-shaped trajectories from single cell data.

Totem package is a tool designed to facilitate inference of tree-shaped trajectories from single-cell data [1]. These include linear, bifurcating, multifurcating, and other tree-shaped trajectories. Totem uses Slingshot [2] to find linear curves through the lineages of the tree.

The easiest way to install Totem is to use either remotes or devtools R package with the install_github command. The dynplot and dynfeature R packages are not available on CRAN, and they must be installed from GitHub.

remotes::install_github("dynverse/dynfeature")
remotes::install_github("dynverse/dynplot")

remotes::install_github("elolab/Totem")

The HTML version of the R package vignette can be accessed here.

[1] Johannes Smolander, Sini Junttila, Laura L Elo, Cell-connectivity-guided trajectory inference from single-cell data, Bioinformatics, Volume 39, Issue 9, September 2023, btad515, https://doi.org/10.1093/bioinformatics/btad515

[2] Street, K., Risso, D., Fletcher, R. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018). https://doi.org/10.1186/s12864-018-4772-0