From 5c0a3e7f83923a71c0448186a46e8fa94e59303a Mon Sep 17 00:00:00 2001 From: Steven Wu Date: Thu, 15 Sep 2016 15:01:49 -0700 Subject: [PATCH] Add ToC to README.md (#191) - Add `table of content` to help users to navigate around this long file. - The ToC is generated by using `https://github.com/ekalinin/github-markdown-toc` --- README.md | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a6328d3b..7759ae23 100644 --- a/README.md +++ b/README.md @@ -7,6 +7,23 @@ Authors: Don Conrad, Avinash Ramu, Kael Dai, and Reed A. Cartwright. DeNovoGear is a software package to detect *de novo* mutations using next-generation sequencing data. It supports the analysis of many differential experimental designs and uses advanced statistical models to reduce the false positve rate. +## Table of Contents +* [INSTALLATION](#installation) + * [Download](#download) + * [Compiling](#compiling) + * [Installation](#installation-1) + * [Testing](#testing) +* [RUNNING THE CODE](#running-the-code) + * [Synposis](#synposis) + * [dng call: Finding Mutations in General Pedigrees](#dng-call-finding-mutations-in-general-pedigrees) + * [dng dnm: Finding Denovo Mutations in trios and pairs.](#dng-dnm-finding-denovo-mutations-in-trios-and-pairs) + * [Separate models for the X chromosome](#separate-models-for-the-x-chromosome) + * [PAIRED SAMPLE ANALYSIS](#paired-sample-analysis) + * [PHASER](#phaser) + * [General options for TRIOs and Paired Sample Calling](#general-options-for-trios-and-paired-sample-calling) +* [RELEASE NOTES](#release-notes) +* [DEPENDENCIES](#dependencies) +* [ACKNOWLEDGEMENTS](#acknowledgements) ## INSTALLATION @@ -390,7 +407,7 @@ DNG contains code to [download and build missing dependencies](#build-missing-de ### dng treecall: Finding Mutations and Trees from Single Cell Sequencing -`dng treecall` is an experimental module to identify mutations and trees from whole-genome sequencing of single cells +`dng treecall` is an experimental module to identify mutations and trees from whole-genome sequencing of single cells #### Usage: