updated README file

README.md

@@ -2,42 +2,50 @@
 
 ![Unit tests](https://github.com/baliga-lab/miner3/actions/workflows/python-test.yml/badge.svg)
 
-mechanistic inference of node-edge relationships
+**M**echanistic **I**nference of **N**ode-edge **R**elationships
 
-# Docker image
+## Usage
+
+### Docker image
 
 you can access a Docker image with a full MINER installation at  Docker Hub with the name ```weiju/isb-miner3```
 
 ```
 $ docker pull weiju/isb-miner3
 ```
 
+### Through pip
+
+```
+$ pip install isb-miner3
+```
 
-# Tools documentation
+## Command Line Tools documentation
 
 Please see command line documentation at https://baliga-lab.github.io/miner3/
 
-# tutorial information
+## Tutorial information
 
-A template with instructions and code for performing a miner analysis is provided in the miner/src directory. 
+Find a walkthrough analysis in the form of a [Jupyter Notebook here](Example MINER Analysis.ipynb)
 
-The template can be opened using Anaconda by selecting jupyter notebook from the user interface, or by simply typing "jupyter notebook" into the command line. 
+## What you need to get started
 
-# what you need to get started
 Before the miner analysis can be performed, the gene expression data to be analyzed must be added to the miner/data directory. Ensure that your expression data is of the form log2(TPM+1) or log2(FPKM+1).
 
-If survival analysis is desired, a survival file must added to the miner/data directory
+	* If survival analysis is desired, a survival file must added to the miner/data directory
+	* If causal analysis is desired, a mutation file must added to the miner/data directory
 
-If causal analysis is desired, a mutation file must added to the miner/data directory
+## Where to put your data
 
-# where to put your data
 miner will search for specific filenames in the miner/data folder. Be sure to update the lines that read your files with the appropriate paths and filenames. Consider using the following names for consistency:
-    1. Name your expression data "expressionData.csv"
+
+	1. Name your expression data "expressionData.csv"
     2. Name your mutation data "mutations.csv" (only for causal analysis)
     3. Name your survival data "survival.csv" (only for survival analysis)
-   
+
 Note that the gene names will be converted to Ensembl Gene ID format
 
-# common mistakes to avoid
-1. miner does not yet support expression data in counts format. Ensure that data is in log2(TPM+1) or log2(FPKM+1) format.
-2. mechanistic inference includes a step that enforces a minimum correlation coefficient. If your results seem too sparse, try decreasing the minCorrelation parameter.
+## Common mistakes to avoid
+
+	1. miner does not yet support expression data in counts format. Ensure that data is in log2(TPM+1) or log2(FPKM+1) format.
+	2. mechanistic inference includes a step that enforces a minimum correlation coefficient. If your results seem too sparse, try decreasing the minCorrelation parameter.