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.
None published for Bioconductor
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
Has tests
Yes
Test-to-code ratio
0.01
testthat edition
–
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 externalGNU make, PhISCS (optional)
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
- Help pages
- 23
- Examples that run
- 100%20 run in a plain check
- Exported functions with examples
- 95%
- Documented parameters
- 98%
- Return-value docs
- 95%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/benstory/mitoclone2 on 2026-10-25.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| LudwigFig7 | – | – | – |
| M_P1 | data.frame | 1,430 × 16 | No other package |
| M_P2 | data.frame | 1,066 × 22 | No other package |
| N_P1 | data.frame | 1,430 × 16 | No other package |
| N_P2 | data.frame | 1,066 × 22 | No other package |
| example.counts | list | 516 elements | No other package |
| sample_example1 | – | – | – |
10 internal objects are bundled for the package's own use and not listed here.
Topics
People
- Benjamin Story author maintainer
- Gregor Mönke author
- Lars Velten author
Cite
Cite this package
Run in R for the authors' entry:
citation("mitoClone2")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nargab/lqae095.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.