updated README.md

README.md

@@ -11,13 +11,13 @@
 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
+docker pull weiju/isb-miner3
 ```
 
 ### Through pip
 
 ```
-$ pip install isb-miner3
+pip install isb-miner3
 ```
 
 ## Command Line Tools documentation
@@ -26,26 +26,26 @@ Please see command line documentation at https://baliga-lab.github.io/miner3/
 
 ## Tutorial information
 
-Find a walkthrough analysis in the form of a [Jupyter Notebook here](Example MINER Analysis.ipynb)
+Find a walkthrough analysis in the form of a [Jupyter Notebook here](Example%20MINER%20Analysis.ipynb)
 
 ## 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 causal analysis is desired, a mutation 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
 
 ## 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"
-    2. Name your mutation data "mutations.csv" (only for causal analysis)
-    3. Name your survival data "survival.csv" (only for survival analysis)
+  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.
+  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.