CDI
Bioc currentClustering Deviation Index (CDI)
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
13 5 exported
Complexity
5.2 avg / 12 max
Call network
13 nodes / 10 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
2,302
Files
40
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
8
Testing & CI
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
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
3.6
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-12-05
Latest release
2026-04-28
Avg cadence
168 days
Cold removal rate
–
Dep drift
0
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
- 15%
Topics
People
- Jiyuan Fang maintainer author
- Cliburn Chan contributor
- Qi-Jing Li contributor
- Kouros Owzar contributor
- Diyuan Qin contributor
- Liuyang Wang contributor
- Jichun Xie contributor