CIMICE
Bioc currentCIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
CIMICE is a tool in the field of tumor phylogenetics and its goal is to build a Markov Chain (called Cancer Progression Markov Chain, CPMC) in order to model tumor subtypes evolution. The input of CIMICE is a Mutational Matrix, so a boolean matrix representing altered genes in a collection of samples. These samples are assumed to be obtained with single-cell DNA analysis techniques and the tool is specifically written to use the peculiarities of this data for the CMPC construction.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
50 48 exported
Complexity
2.4 avg / 10 max
Call network
50 nodes / 37 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
4,416
Files
98
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
50
Internal functions
2
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
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-08-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 53includes a package overview page
- Examples that run
- 100%50 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/redsnic/cimice on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Topics
People
-
Nicolò Rossi
author
maintainer
Lab. of Computational Biology and Bioinformatics, Department of Mathematics, Computer Science and Physics, University…
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CIMICE")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.