Draft Readme.md

README.md

@@ -1,7 +1,38 @@
 # JACUSA2helper
-Auxiliary R package for assessment of JACUSA1.x and JACUSA2.x results
 
-Under construction! 
+## Overview
+
+Auxiliary R package for the assessment of [JACUSA1.x](https://github.com/dieterich-lab/JACUSA) and [JACUSA2.x](https://github.com/dieterich-lab/JACUSA2) results.
+
+TODO
+* successor of [JACUSAhelper](https://github.com/dieterich-lab/JACUSA) -> obsolete
+* Adjust JACUSA Repository -> obsolete
+* new features JACUSA2
+* call-1, call-2, rt-arrest, and variant stratification
+* faster, cleaner, multi-threaded
+
 
 ## Install
 
+Install JACUSA2 helper by either downloading a specific [release](https://github.com/dieterich-lab/JACUSA2helper/releases) or 
+install it directly from the repository via [devtools](https://www.r-project.org/nosvn/pandoc/devtools.html).
+
+### Download
+1. Download JACUSA2helper from [releases](https://github.com/dieterich-lab/JACUSA2helper/releases).
+2. Change to directory where JACUSA2helper was saved.
+2. Start R.
+3. Install downloaded package by issueing: `install.packages("JACUSA2helper")` TODO
+
+### devtools
+[devtools](https://www.r-project.org/nosvn/pandoc/devtools.html)
+1. Start R.
+2. Run install_github("dieterich-lab/JACUSA2helper")
+
+
+## Usage
+`library(JACUSA2helper)`
+
+For more details check the following R Vignettes:
+* General [JACUSA2helper](https://github.com/dieterich-lab/JACUSA2helper/vignette/JACUSA2helper.html) vignette,
+* [Meta conditions](https://github.com/dieterich-lab/JACUSA2helper/vignette/JACUSA2helper-meta-conditions.html) vignette, and
+* TODO