Prepare your environment for Velocity
Create an RStudio project
In the R console run the following commands to install the needed packages to run Velocity
if (!any(rownames(installed.packages()) == "remotes")){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("remotes")
}
library(remotes)
if (!any(rownames(installed.packages()) == "R.utils")){
BiocManager::install("R.utils")
}
library(R.utils)
remotes::install_github('satijalab/seurat-wrappers')
library(SeuratWrappers)
if (!any(rownames(installed.packages()) == "pcaMethods")){
BiocManager::install("pcaMethods")
}
library(pcaMethods)
## For velocito.R you will also need boost and open MP.
## See https://github.com/velocyto-team/velocyto.R
remotes::install_github("velocyto-team/velocyto.R")
library(velocyto.R)
sessionInfo()
Download the template Markdown workshop document for Velocity analysis and open it.
In the R console run the following command
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2021-August-Advanced-Topics-in-Single-Cell-RNA-Seq-Trajectory-and-Velocity/master/data_analysis/Velocyto.Rmd", "Velocyto.Rmd")