instructions_data_analysis_fig5.txt

#Run all the following commands from within "Scripts" directory, unless stated otherwise

## Run the following commands from RStudio Console:
source("diffBUM_HMM_Xist_dataset_no_scaling.R")
source("diffBUM_HMM_Xist_dataset_with_scaling.R")
source("dStruct_Xist_dataset_no_scaling.R")
source("dStruct_Xist_dataset_with_scaling.R")

##Run the following command from within "diff_BUM_HMM/Jupyter_notebooks/Xist analysis/Big_dataframe_SHAPEMAP_BED_for_Xist" directory:
jupyter nbconvert --to script --execute --stdout Updated_code_for_making_big_data_table.ipynb | python