HiFive
Introduction
HiFive Overview
Organization of the HiFive package
Getting started
Installing HiFive
Installing Documentation
Restriction Fragment Handling
Loading 5C Fragments
Loading HiC Fends
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
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
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 plotting module
HiFive
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v: 1.0.3
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