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.
None published for Bioconductor
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
93
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
22
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
–
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
- Help pages
- 36includes a package overview page
- Examples that run
- 92%22 run in a plain check · 2 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/dozmorovlab/hiccompare on 2026-10-22.
GitHub Pages site last deployed 2020-08-27
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| HMEC.chr10 | data.frame | 35,386 × 3 | No other package |
| HMEC.chr22 | data.frame | 2,490 × 3 | No other package |
| NHEK.chr10 | data.frame | 35,510 × 3 | No other package |
| NHEK.chr22 | data.frame | 2,508 × 3 | No other package |
| brain_table | list | 2 elements | No other package |
| centromere_locations | data.frame | 24 × 3 | No other package |
| cooler | data.frame | 217,230 × 7 | No other package |
| hg19_blacklist | data.frame | 1,649 × 3 | No other package |
| hg38_blacklist | data.frame | 38 × 3 | No other package |
| hmec.IS | – | – | – |
| nhek.IS | – | – | – |
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' entry:
citation("HiCcompare")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-018-2288-x.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.