SpotClean
Bioc currentSpotClean adjusts for spot swapping in spatial transcriptomics data
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
44 11 exported
Complexity
3 avg / 14 max
Call network
44 nodes / 28 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
3,588
Files
46
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
33
Testing & CI
Has tests
Yes
Test-to-code ratio
0.21
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
4.2.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-22
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
- 0%
Topics
People
- Zijian Ni author maintainer
- Christina Kendziorski contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SpotClean")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
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.