scHiCcompare
Bioc currentDifferential Analysis of Single-cell Hi-C Data
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
This package provides functions for differential chromatin interaction analysis between two single-cell Hi-C data groups. It includes tools for imputation, normalization, and differential analysis of chromatin interactions. The package implements pooling techniques for imputation and offers methods to normalize and test for differential interactions across single-cell Hi-C datasets.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
24 9 exported
Complexity
4.1 avg / 11 max
Call network
24 nodes / 29 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
4,085
Files
68
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
15
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.02
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
4.5.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-04-15
Latest release
2026-04-28
Avg cadence
189 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 25%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/dozmorovlab/schiccompare on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| MG.bandnorm_chr20_1 | data.frame | 269 × 5 | No other package |
| MG.bandnorm_chr20_10 | data.frame | 329 × 5 | No other package |
| MG.bandnorm_chr20_2 | data.frame | 308 × 5 | No other package |
| MG.bandnorm_chr20_3 | data.frame | 314 × 5 | No other package |
| MG.bandnorm_chr20_4 | data.frame | 122 × 5 | No other package |
| MG.bandnorm_chr20_5 | data.frame | 262 × 5 | No other package |
| MG.bandnorm_chr20_6 | data.frame | 275 × 5 | No other package |
| MG.bandnorm_chr20_7 | data.frame | 232 × 5 | No other package |
| MG.bandnorm_chr20_8 | data.frame | 269 × 5 | No other package |
| MG.bandnorm_chr20_9 | data.frame | 309 × 5 | No other package |
| ODC.bandnorm_chr20_1 | data.frame | 335 × 5 | No other package |
| ODC.bandnorm_chr20_10 | data.frame | 286 × 5 | No other package |
| ODC.bandnorm_chr20_2 | data.frame | 345 × 5 | No other package |
| ODC.bandnorm_chr20_3 | data.frame | 242 × 5 | No other package |
| ODC.bandnorm_chr20_4 | data.frame | 228 × 5 | No other package |
| ODC.bandnorm_chr20_5 | data.frame | 156 × 5 | No other package |
| ODC.bandnorm_chr20_6 | data.frame | 387 × 5 | No other package |
| ODC.bandnorm_chr20_7 | data.frame | 336 × 5 | No other package |
| ODC.bandnorm_chr20_8 | data.frame | 389 × 5 | No other package |
| ODC.bandnorm_chr20_9 | data.frame | 379 × 5 | No other package |
| scHiC.table_MG_chr22 | data.frame | 666 × 14 | No other package |
| scHiC.table_ODC_chr22 | data.frame | 666 × 14 | No other package |
Topics
People
- My Nguyen author maintainer
- Mikhail Dozmorov author
Cite
Cite this package
Run in R for the authors' entry:
citation("scHiCcompare")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2024.11.06.622369.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.