Day 3 Pre-reading

Below are the papers associated with the R packages we will be using for Day 3 of the workshop.

CytoTRACE2

Link: Improved reconstruction of single-cell developmental potential with CytoTRACE 2

Monocle

Link: The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

CellChat

Link: CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics

clusterProfiler

Link: clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

decoupleR

Link: decoupleR: ensemble of computational methods to infer biological activities from omics data Open Access