megadepth
Bioc currentmegadepth: BigWig and BAM related utilities
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 10 exported
Complexity
2.9 avg / 8 max
Call network
18 nodes / 16 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
2,247
Files
71
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
10
Internal functions
8
Testing & CI
Has tests
Yes
Test-to-code ratio
0.56
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
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
1
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2021-02-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 91%
- Return-value docs
- 100%
- References docs
- 25%
Topics
Depended on by (3)
Bioconductor (3)
People
- David Zhang author maintainer
- Leonardo Collado-Torres author