ccfindR
Bioc currentCancer Clone Finder
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
A collection of tools for cancer genomic data clustering analyses, including those for single cell RNA-seq. Cell clustering and feature gene selection analysis employ Bayesian (and maximum likelihood) non-negative matrix factorization (NMF) algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses, including meta-gene identification, visualization, and construction of rank-based trees for clusters.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
49 26 exported
Complexity
5.8 avg / 31 max
Call network
49 nodes / 30 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
5,721
Files
83
Compiled share
2.3%
Has compiled src
Yes
Language breakdown
API
Exported functions
37
Internal functions
20
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
5.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
C++11
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 60includes a package overview page
- Examples that run
- 100%45 run in a plain check
- Exported functions with examples
- 92%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 3% with a bibliography file
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
Topics
Suggested by (1)
People
- Jun Woo author maintainer
- Jinhua Wang author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ccfindR")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.