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.
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
2,196
Files
41
Compiled share
24.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
9
Internal functions
10
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.05
testthat edition
3
CI present
No
CI type
[]
PR gated
No
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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
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' preferred citation:
citation("ccImpute")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
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