HiFive’s documentation

Contents:

• Introduction
  • HiFive Overview
  • Organization of the HiFive package
  • Release History
• Getting started
  • Installing HiFive
  • Installing Documentation
• Restriction Fragment Handling
  • Loading 5C Fragments
  • Loading HiC Fends
  • Non-restriction Fragment-based Genome Partitions
• Loading Data
  • Loading 5C data
  • Loading HiC Data
• Filtering Data
  • 5C Filtering
  • HiC Filtering
• Distance-Dependence Estimation
  • 5C Distance-Dependence Estimation
  • HiC Distance-Dependence Estimation
• Normalizing Data
  • Probability Algorithm
  • Express Algorithm
  • Binning Algorithm
  • Chaining Normalization Approaches
• Binning Strategies
  • The ‘upper’ format
  • The ‘full’ format
  • The HiC ‘compact’ format
  • The 5C ‘compact’ format
  • Dynamic Binning
• Multi-Resolution Heatmap
  • MRH Approach
  • Standalone MRH program
  • File specs
• QuASAR Hi-C Scoring
• Using HiFive
  • 5C Subcommands
  • 5C Options
  • HiC Subcommands
  • HiC Options
• Tutorial for 5C Classes
  • Creating a Fragment object
  • Creating a FiveCData object
  • Creating a FiveC project object
  • Filter 5C fragments
  • Find 5C distance function
  • Learn 5C normalization parameters
  • Generating a heatmap
  • Accessing heatmap data
  • Plotting a heatmap
• Tutorial for HiC Classes
  • Creating a Fend object
  • Creating a HiCData object
  • Creating a HiC project object
  • Filter HiC fends
  • Find HiC distance function
  • Learn HiC normalization parameters
  • Generating a heatmap
  • Accessing heatmap data
  • Plotting a heatmap
  • Creating a multi-resolution heatmap
  • Determining sample quality
• HiFive’s API
  • The Fragment class
  • The Fend class
  • The FiveCData class
  • The HiCData class
  • The FiveC class
  • The HiC class
  • The fivec_binning module
  • The hic_binning module
  • The quasar module
  • The plotting module
• Release History
  • 1.5 (2017-08-15)
  • 1.4 (2017-06-28)
  • 1.3 (2016-04-28)
  • 1.2.2 (2015-12-15)
  • 1.2 (2015-10-21)
  • 1.1 (2015-08-26)
  • 1.0.3 (2015-04-23)
  • 1.0.2 (2015-04-16)

Indices and tables

• Index
• Module Index
• Search Page