ChromSCape
Bioc currentAnalysis of single-cell epigenomics datasets with a Shiny App
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
141 83 exported
Complexity
4.9 avg / 25 max
Call network
141 nodes / 121 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
14,813
Files
484
Compiled share
0.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
82
Internal functions
55
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
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
99
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
17
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 91%
- Documented parameters
- 97%
- Return-value docs
- 100%
- References docs
- 4%
Topics
People
- Pacome Prompsy author maintainer
- Celine Vallot author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ChromSCape")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.