HiCcompare
Bioc currentHiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
55 24 exported
Complexity
4.3 avg / 25 max
Call network
55 nodes / 35 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
5,538
Files
95
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
22
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 92%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (4)
Bioconductor (4)
People
- Mikhail Dozmorov author maintainer
- Kellen Cresswell author
- John Stansfield author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HiCcompare")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.