fix typo, update install instructions

docs/about.md

@@ -11,7 +11,7 @@ The authors performed a longitudinal transcriptomic analysis using scRNA-sequenc
 The data includes 12 whole lung samples across pre- and post- intratracheal silica. 35 unique cell states were identified using highly and specifically expressed marker genes. For simplicity, we are splitting samples into 2 levels: exposed and not exposed. The goal is to identify which cell types are differentially abundant post-silica exposure. 
 
 ```
-cds = readRDS("silicosis_cds.cds")
+cds = readRDS("silicosis_cds.rds")
 
 # for simplicity, we are lumping together pre and post i.t. silica
 colData(cds)$exposed = ifelse(colData(cds)$Timepoint == 0, "not exposed", "exposed")

docs/install.md

@@ -12,12 +12,11 @@ Hooke builds on top of the [Monocle3 package](https://cole-trapnell-lab.github.i
 devtools::install_github("cole-trapnell-lab/monocle3")
 ```
 
-Hooke depends on the [PLNmodels package](https://pln-team.github.io/PLNmodels/index.html). Currently we are using a forked version of the PLNmodels package until our pull request is approved. 
-
-Use the github install: 
+Hooke depends on the [PLNmodels package](https://pln-team.github.io/PLNmodels/index.html). 
+You can install as follows: 
 
 ```r
-devtools::install_github("cole-trapnell-lab/PLNmodels")
+remotes::install_github("pln-team/PLNmodels")
 ```
 
 Finally, install the hooke package as follows: 
@@ -26,5 +25,11 @@ Finally, install the hooke package as follows:
 devtools::install_github("cole-trapnell-lab/hooke")
 ```
 
+If you wish to install the develop branch of hooke, execute: 
+
+```r
+devtools::install_github("cole-trapnell-lab/hooke", ref="develop")
+```
+
 See our [Github repository](https://github.com/cole-trapnell-lab/hooke) for more details.