SC_Course_May9

Trajectory analysis

This week we'll walk through some trajectory analysis in R.

Both packages are available in Bioconductor.

Literature of interest:
  Monocle3: https://cole-trapnell-lab.github.io/monocle3/papers/
  Slingshot:  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4772-0
  Wide comparision of trajectory methods: https://www.nature.com/articles/s41587-019-0071-9

Information:
   Monocle3 home page: https://cole-trapnell-lab.github.io/monocle3/
   Slingshot home page: https://github.com/kstreet13/slingshot

Installation:
  Monocle3: https://cole-trapnell-lab.github.io/monocle3/docs/installation/ 
  Slingshot: https://github.com/kstreet13/slingshot

Tutorials:
   Monocle3:   https://cole-trapnell-lab.github.io/monocle3/docs/getting_started/
   Slingshot:  https://bioconductor.org/packages/devel/bioc/vignettes/slingshot/inst/doc/vignette.html


Coming up: Multiomics and single-cell ATAC-seq data 

Signac: https://stuartlab.org/signac/
Signac/Seurat multi-omics:  https://stuartlab.org/signac/articles/pbmc_multiomic