HiCDOC
Bioc currentA/B compartment detection and differential analysis
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
HiCDOC normalizes intrachromosomal Hi-C matrices, uses unsupervised learning to predict A/B compartments from multiple replicates, and detects significant compartment changes between experiment conditions. It provides a collection of functions assembled into a pipeline to filter and normalize the data, predict the compartments and visualize the results. It accepts several type of data: tabular `.tsv` files, Cooler `.cool` or `.mcool` files, Juicer `.hic` files or HiC-Pro `.matrix` and `.bed` files.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
103 21 exported
Complexity
3.6 avg / 14 max
Call network
103 nodes / 146 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
9,258
Files
159
Compiled share
9.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
30
Internal functions
48
Testing & CI
Has tests
Yes
Test-to-code ratio
0.15
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
5.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
1
C++ standard
–
License
LGPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 88%
- Documented parameters
- 98%
- Return-value docs
- 96%
- References docs
- 0%
Topics
People
- Maigné Élise author maintainer
- Kurylo Cyril author
- Zytnicki Matthias author
- Foissac Sylvain author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HiCDOC")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 v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.