Update README.md

README.md

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 # RNAFracQuant - RNA Fraction Quantification
 Employ a bayesian statistical model to quantify the distribution of mRNA in different fractions after centrifugation of subcellular components.
 
-# Contents
-
 ------------
 
-# 1. Introduction
+# Introduction
 This vignette introduces how to use the functions in this packge. This package employs a bayesian statistical model to quantify the distribution of mRNA in Saccharomyces Cerevisiae cells. The whole idea is based on this heat shock experiment:
 
 *"To prepare RNA-seq data, cells are fractionated before cloning the resulting RNA into cDNA libraries. Then after centrifugation, granules with large molecular weight would deposit at the bottom and the others remain in the supernatant. Total transcripts and transcripts in the two factions (Supernatant, Pellet) are measured respectively both before and after heat shock. Therefore, for each transcript, we have a basic formula $N_{total} = N_{pellet} + N_{supernatant}$."*
@@ -14,7 +12,7 @@ This vignette introduces how to use the functions in this packge. This package e
 
 -----------
 
-## 1.1 Required input files and their format
+## Required input files and their format
 Users need to provide count files and a samplesheet file. Those files need to meet the conditions below:
 
 **<span style="color:red;">1.</span> Both count files and samplesheet file need to be in the ".txt" format**  
@@ -27,7 +25,7 @@ Functions in this package are linked to each other. We aim to output the proport
 
 -----------
 
-# 2. Installation
+# Installation
 
 We recommand you to use package "devtools" for dowloading this package from GitHub. Please refer [devtools installation instructions](https://www.r-project.org/nosvn/pandoc/devtools.html) for more information.
 
@@ -44,7 +42,7 @@ library(RNAFracQuant)
 
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-# 3. View vignettes or documentation
+# View vignettes or documentation
 
 R will load the knitr package to build these vignettes to HTML files, and you can see them when you type the commands lines:
 ```
@@ -57,7 +55,7 @@ browseVignettes("RNAFracQuant")
 
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-## 3.1 Quick guide
+## Quick guide
 
 If you only want to get the pSup values for transcripts, the code below shows you the quickest way to get them with **RNAFracQuant**.
 ```
@@ -70,5 +68,5 @@ write_results(result_data)
 
 
 
-# 4. Issues update
+# Issues update
 If you get any problems with this package, you could update your questions [here](https://github.com/thebestecho/demo-RNAFracQuant/issues).