install instructions

install.md

@@ -0,0 +1,61 @@
+# Installing and running the app:
+
+1. Install Rstudio for your operating system. 
+
+    https://rstudio.com/products/rstudio/download/#download
+
+2. Install R version 3.6.2
+    - windows: https://cran.r-project.org/bin/windows/base/
+    - macosx: https://cran.r-project.org/bin/macosx/R-3.6.2.pkg
+    - linux: `sudo apt install r-base`
+
+3. Open RStudio and point it to the newest version of R (only applicable if you have an old version of R installed)
+
+4. Install the following packages by running these lines in your R console:
+    (shown in the image in the bottom left hand corner)
+    ![](.install_images/r_console.png)
+
+    ```
+    if (!any(rownames(installed.packages()) == "shiny")){
+      install.packages("shiny")
+    }
+    library(shiny)
+    
+    if (!any(rownames(installed.packages()) == "markdown")){
+      install.packages("markdown")
+    }
+    library(markdown)
+    
+    if (!any(rownames(installed.packages()) == "ggplot2")){
+      if (!requireNamespace("BiocManager", quietly = TRUE))
+          install.packages("BiocManager")
+      BiocManager::install("ggplot2")
+    }
+    library(ggplot2)
+    
+    if (!any(rownames(installed.packages()) == "dplyr")){
+      if (!requireNamespace("BiocManager", quietly = TRUE))
+          install.packages("BiocManager")
+      BiocManager::install("dplyr")
+    }
+    library(dplyr)
+    
+    
+    if (!any(rownames(installed.packages()) == "Seurat")){
+      if (!requireNamespace("BiocManager", quietly = TRUE))
+          install.packages("BiocManager")
+      BiocManager::install("Seurat")
+    }
+    library(Seurat)
+    ```
+
+5. Download the contents of the app: https://github.com/ucdavis-bioinformatics/scRNA_shiny/archive/master.zip
+    - move it somewhere convenient like your Desktop
+    
+6. File > Open project in Rstudio. Then choose wherever you moved this folder. 
+![](.install_images/open_project.png)
+
+7. Move the file of interest (.rds) supplied to you to this same directory. Then change the highligted line to be the name of the your file.
+![](.install_images/line_change.png)
+(finally click run app at the top of the page after clicking on the app.R file of the right hand side of the GUI)
+![](.install_images/run_app.png)