fRagmentomics
Bioc currentExtract Fragmentomics Features and Mutational Status
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
A user-friendly R package that enables the characterization of each cfDNA fragment overlapping one or multiple mutations of interest, starting from a sequencing file containing aligned reads (BAM file). fRagmentomics supports multiple mutation input formats (e.g., VCF, TSV, or string "chr:pos:ref:alt" representation), accommodates one-based and zero-based genomic conventions, handles mutation representation ambiguities, and accepts any reference file and species in FASTA format. For each cfDNA fragment, fRagmentomics outputs its size, its 3' and 5' sequences, and its mutational status. Optionally, when users set apply_bcftools_norm = TRUE, fRagmentomics invokes the external command-line tool bcftools norm to left-align and normalize variants. If bcftools is not found on the system PATH while this option is enabled, the function errors. The package does not install external software; see the INSTALL file for per-OS instructions.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
66 5 exported
Complexity
9.2 avg / 66 max
Call network
66 nodes / 68 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
13,092
Files
120
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
60
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
1.11
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
4.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 69%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Killian Maudet author maintainer
- Elsa Bernard author
- Yoann Pradat author
- Juliette Samaniego author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("fRagmentomics")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.