mCSM Analysis
=============

This repo does mCSM analysis using Python, bash and R.

Requires an additional 'Data' directory. Batteries not included.

## Assumptions

 1. git repos are cloned to `~/git`
 2. Requires a `Data/` in `~/git` which has the struc created by `mk-drug-dirs.sh` 

## LSHTM\_analysis: 
 
subdirs within this repo

```
 meta\_data\_analysis/
 	*.R
 	*.py
	
 mcsm\_analysis/
	<drug>/ (generated by `meta_data_analysis/pnca_data_extraction.py`. To be replaced with command line args or config option "soon")
		scripts/
		*.R
		*.py
			mcsm/
			*.sh
			*.py
			*.R
			plotting/
			*.R
```

More docs here as I write them.