Welcome to HiC1Dmetrics’s documentation!

Contents:

• 1. Overview and Installation
  • 1.1 Introduction
  • 1.2 Installation
  • 1.3 Requirements
  • 1.4 Test file
  • 1.5 Input format
  • 1.6 Overall usage
  • 1.7 Memory requirement
• 2. Calculate 1D metrics for one sample
  • 2.1 Quick start
  • 2.2 Usage
  • 2.3 Calculate 1D metrics (one-sample)
  • 2.4 Visulize 1D metrics (one-sample)
• 3. Calculate 1D metrics for comparison of two samples
  • 3.1 Quick start
  • 3.2 Usage
  • 3.3 Calculate 1D metrics (two-sample)
  • 3.4 Visualize 1D metrics (two-sample)
• 4. Extract secondary information from metrics (dTAD, stripeTAD, etc.)
  • 4.1 Quick start
  • 4.2 Parameters
  • 4.3 dTAD
  • 4.4 stripe
  • 4.5 stripe-TAD
  • 4.6 Hubs
  • 4.7 TAD
• 5. Obtain the same metrics for muliple samples
  • 5.1 Calculation
  • 5.2 Parameters
  • 5.3 Visualization
  • 5.4 Statistically comparison
• 6. Obtain various types of 1D metrics for the same sample
  • 6.1 Calculation
  • 6.2 Parameters
  • 6.3 Visuliazation
• 7. Provide basic functions to visualize and handle Hi-C data
  • 7.1 Plot indicated region
  • 7.2 Make contact matrix.
  • 7.3 Make gene density file for PC1

Indices and tables

• Index

• Module Index

• Search Page