Add scripts and formatting

Author: clarepacini

README.md

@@ -3,39 +3,41 @@ Code for integration and evaluation of Broad and Sanger Institutes CRISPR-Cas9 s
 
 
 The code should be executed in the following order:
-GenerateSourceData.R
-Figure2.R
-Figure3.R
-UseCaseEssNonEss.R
-CalculateNormLRT.R
-UseCaseLineageSubtypes.R
-UseCaseBiomarkers.R
-CalculateBinaryDepletions.R
-
+* GenerateSourceData.R
+* Figure2.R
+* Figure3.R
+* UseCaseEssNonEss.R
+* CalculateNormLRT.R
+* UseCaseLineageSubtypes.R
+* UseCaseBiomarkers.R
+* CalculateBinaryDepletions.R
+* IntegratedPerformance.R
+* DownSamplingBatchCorrection.R
+* DownSamplingFigures.R
 
 To run the code, source data files should be downloaded from the Figshare repository: 
-The location of the Figshare directory should be added to the R scripts as indicated (dir.Input variable).
+The location of the Figshare directory should be added to the R scripts as indicated (dir.Input variable). Note the DownSamplingBatchCorrection script is set to run in parallel over 24 cores. This script is computationally expensive.
 
 The packages required to run the R scripts are:
-here
-preprocessCore
-stringr
-RColorBrewer
-colorspace
-scales
-psych
-sva
-ggfortify
-VennDiagram
-splines
-e1071
-tsne
-caTools
-ggplot2
-gridExtra
-magrittr
-tidyverse
-dplyr
-MASS
-sn
-beeswarm
+* here
+* preprocessCore
+* stringr
+* RColorBrewer
+* colorspace
+* scales
+* psych
+* sva
+* ggfortify
+* VennDiagram
+* splines
+* e1071
+* tsne
+* caTools
+* ggplot2
+* gridExtra
+* magrittr
+* tidyverse
+* dplyr
+* MASS
+* sn
+* beeswarm