RNA velocity estimation in R
The easiest way to install velocyto.R is using devtools::install_github() from R:
library(devtools)
install_github("velocyto-team/velocyto.R")
You need to have boost (e.g. sudo apt-get install libboost-dev) and openmp libraries installed.
The example shows how to annotate SMART-seq2 reads from bam file and estimate RNA velocity.
The example shows how to load spliced/unspliced matrices from loom files prepared by velocyto.py CLI, use pagoda2 to cluster/embed cells, and then visualize RNA velocity on that embedding.
This example shows how to start analysis using dropEst count matrices, which can calculated from inDrop or 10x bam files using dropEst pipeline. It then uses pagoda2 to cluster/embed cells, and then visualize RNA velocity on that embedding.