Holding2019.Rmd

---
title: "Holding2019"
author: "Markowetzlab"
output: html_document
---

Install and load the package.


```{r}
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.

```{r}
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.  

```{r}
set.seed(42)
mnem_dixit2016_K562_lowmoi()
```

Generate Figure 6 from Holding2019 that shows the knockdown efficiency.  

```{r}
knockdown_efficiency()
```