mitoClone2
Bioc currentClonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 21 exported
Complexity
3.9 avg / 12 max
Call network
49 nodes / 35 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
4,336
Files
75
Compiled share
9.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
22
Internal functions
21
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.01
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
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
2
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
1
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
- 98%
- Return-value docs
- 95%
- References docs
- 0%
Topics
People
- Benjamin Story author maintainer
- Gregor Mönke author
- Lars Velten author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("mitoClone2")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 v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.