cfDNAPro
Bioc currentcfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
74 15 exported
Complexity
3.4 avg / 13 max
Call network
74 nodes / 47 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
4,367
Files
67
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
48
Testing & CI
Has tests
Yes
Test-to-code ratio
0.02
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
0
Dep constraint coverage
36.8%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
10
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 87%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Haichao Wang author maintainer
- Elkie Chan contributor
- Tomer Kaplan contributor
- Florian Markowetz contributor
- Nitzan Rosenfeld contributor
- Christopher Smith contributor
- Hui Zhao contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("cfDNAPro")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.