multiHiCcompare
Bioc currentNormalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 16 exported
Complexity
6 avg / 24 max
Call network
31 nodes / 16 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
4,264
Files
80
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
15
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.04
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
4.0.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2018-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 34
- Examples that run
- 86%19 run in a plain check · 3 never run
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- juiceboxVisualization HTML
- multiHiCcompare HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/dozmorovlab/multihiccompare on 2026-10-25.
GitHub Pages site last deployed 2020-11-23
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| HCT116_r1 | data.frame | 56,603 × 4 | No other package |
| HCT116_r2 | data.frame | 57,010 × 4 | No other package |
| HCT116_r3 | data.frame | 56,744 × 4 | No other package |
| HCT116_r4 | data.frame | 54,307 × 4 | No other package |
| HCT116_r5 | data.frame | 55,092 × 4 | No other package |
| HCT116_r6 | data.frame | 55,581 × 4 | No other package |
| hg19_cyto | – | – | – |
| hg38_cyto | – | – | – |
| hicexp2 | – | – | – |
| hicexp_diff | – | – | – |
Topics
Depended on by (2)
Suggested by (1)
People
- Mikhail Dozmorov author maintainer
- John Stansfield author
Cite
Cite this package
Run in R for the authors' entry:
citation("multiHiCcompare")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/btz048.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.