decontX
Bioc currentDecontamination of single cell genomics data
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
82 7 exported
Complexity
3.3 avg / 17 max
Call network
82 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
6,713
Files
54
Compiled share
32.9%
Has compiled src
Yes
Language breakdown
API
Exported functions
10
Internal functions
39
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
25%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
1 externalGNU make
C++ standard
C++17
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-10-24
Latest release
2026-04-28
Avg cadence
189 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
- Help pages
- 17includes a package overview page
- Examples that run
- 100%9 run in a plain check
- Exported functions with examples
- 89%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 6%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
2 practices detected in the Bioconductor git repository
Topics
People
- Joshua Campbell author maintainer
- Masanao Yajima author
- Yuan Yin author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("decontX")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 v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.