In markowetzlab/SCperturb: Data package for various single cell perturbation experiments

Install and load the package.

devtools::install_github("markowetzlab/SCperturb")
library(SCperturb)

List available data. 3 data objects are included for each project: counts.project, rowmetadata.project and colmetadata.project.

SCperturb::listprojects()
data(rowmetadata.datlinger2017_stim)

Generate Figure 9 from Holding2019 "Network reconstruction from single cell transcriptomic profiles of CRISPR gene perturbations". This takes about an hour to run, as it calculates differential expression and then runs mnem.

set.seed(42)
mnem_dixit2016_K562_lowmoi()

Generate Figure 6 from Holding2019 that shows the knockdown efficiency.

knockdown_efficiency()

markowetzlab/SCperturb documentation built on Nov. 9, 2019, 1:52 p.m.