`chr3d` API Reference

Chr3D is a Python framework for 3D chromatin interaction analysis. The package exposes a uniform top-level import — every pipeline, processing step, and utility is accessible from a single namespace.


import chr3d as c3d

This reference documents the stable public API of chr3d v3.2.0. All classes and functions listed here are importable from chr3d or one of its sub-packages (chr3d.hic, chr3d.peak_based, chr3d.utils).

Package layout

Pipelines at a glance

Pipeline	Module	Input	Output
Bulk Hi-C	`HiCPipeline`	paired FASTQ	`.cool`, `.mcool`, TADs, loops, compartments
Single-nucleus Hi-C	`SnHiCPipeline`	list of per-cell FASTQs	per-cell `.cool`, pseudobulk `.mcool`
ChIA-PET	`ChiaPetPipeline`	paired FASTQ + linkers	peaks + significant loops
HiChIP	`HiChIPPipeline`	paired FASTQ + fragment BED	peaks + significant loops

Low-level building blocks

Every pipeline is composed of standalone, modular step-classes that can be used independently when you need finer control than the orchestrators provide:

Category	Classes
Alignment & SAM/BAM	`HiCAligner`, `HiCSamProcessor`, `PETMapperV3`
Pairs / BEDPE	`HiCPairsProcessor`
Contact matrices	`HiCMatrixGenerator`
Linker filtering	`LinkerFilterV3`
Peak calling	`PeakCaller`
Fragment digest / purification	`RestrictionSiteGenerator`, `FragmentIndex`, `purify_bedpe`
Loop calling (statistical)	`classify_pets`, `extract_templates`, `BackgroundSamplingPhase1`, `calculate_pvalues`, `apply_fdr_corrections`
Quality control	`HiCQCAnalyzer`
Data preparation	`FastqSplitter`
Visualisation export	`loops_to_beddb`
QC / detection	`detect_restriction_enzyme`

Conventions used in this reference

Every class signature is shown in the form class chr3d.X(param1, param2=default, ...).
Every method signature is shown as MethodName(param1, param2, ...) → ReturnType.
Parameters that accept None are marked optional.
Default values shown match the source code exactly.
All paths are strings; all thread/core counts are ints.

Entry points

Import pattern	Example
Top-level	`import chr3d as c3d; c3d.HiCPipeline(...)`
Sub-package	`from chr3d.hic import HiCPipeline`
Utils function	`from chr3d.utils import loops_to_beddb`
Background model	`from chr3d.peak_based.background_model import classify_pets`

For a CLI-based interface, see chr3d --help (entry point registered in pyproject.toml).

chr3d API Reference