DenoIST
Bioc currentDenoIST: Denoising Image-based Spatial Transcriptomics data
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
DenoIST identifies and removes contamination in Image-based Spatial Transcriptomics data, using a transposed poisson mixture model with local neighbourhood offsets to infer genes that are likely to be due to neighbourhood contamination rather than endogenous expression.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
4 4 exported
Complexity
11.5 avg / 14 max
Call network
4 nodes / 3 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
1,304
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
0
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.26
testthat edition
–
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
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 4
- Examples that run
- 100%4 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- denoist_spe HTML
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/aaronkwc/denoist on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| example_spe | – | – | – |
| result | list | 3 elements | No other package |
| tx_sub | data.frame | 10 × 11 | No other package |
Topics
People
- Aaron Kwok author maintainer
- Davis McCarthy author
- Heejung Shim author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("DenoIST")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 v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.