B: Analysis – OSCA resources, etc.

Vincent J. Carey, stvjc at channing.harvard.edu

March 27, 2023

Source: vignettes/B_Analysis.Rmd

Example

Trajectory chapter

The OSCA book is built from R markdown files in packages

In principle, you can reproduce any computations in the book, and have instances of all created objects in your workspace via

dir(system.file("book", package="OSCA.advanced"))
pa = dir(system.file("book", package="OSCA.advanced"), full=TRUE)
trajpa = grep("traject", pa, value=TRUE)
library(knitr)
purl(trajpa)
source("trajectory.R", echo=TRUE)

QC

Full testing on devel branch book image

Reaching across: scvi-tools

My efforts at bridging to products of the VI team (Yosef lab) in scviR