Single-cell trajectories

Theory session

Practical session

Download the data: https://drive.google.com/file/d/1eYDUry72RmQTz1t56DpXVUgkd7oEDaoq

Unzip and put into the ‘data’ folder

① Quantification (Including RNA velocity): 1_quantify.Rmd (html), tutorial I followed: https://bustools.github.io/BUS_notebooks_R/velocity.html

② Preprocessing including RNA velocity: 2_preprocessing.Rmd (html)

③ Trajectory analysis using slingshot: 3_slingshot.Rmd (html)

④ Velocity analysis using velocyto.R: 4_velocity.Rmd (html)

We make use of several packages which should have already been installed using the install_packages.R script. Several of these packages are located on github only (but most will be available in the next Bioconductor release). These packages are:

BUStools/BUSpaRse
velocyto-team/velocyto.R
satijalab/seurat-wrappers
dynverse/tradeSeq