ccImpute
Bioc currentccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
41 8 exported
Complexity
2.1 avg / 9 max
Call network
41 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
2,193
Files
37
Compiled share
24.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
9
Internal functions
10
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
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
C++11
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2023-01-19
Latest release
2026-04-28
Avg cadence
176 days
Cold removal rate
–
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 18 (1 internal)
- Examples that run
- 100%8 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/khazum/ccimpute on 2026-10-25.
No development-tooling practices detected in the upstream repository.
Topics
People
- Marcin Malec maintainer author
- Mehmet Dalkilic author
- Hasan Kurban author
- Parichit Sharma author
Cite
Cite this package
Run in R for the authors' entry:
citation("ccImpute")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s12859-022-04814-8.
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.