imcRtools
Bioc currentMethods for imaging mass cytometry data analysis
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
71 23 exported
Complexity
9.3 avg / 56 max
Call network
71 nodes / 61 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
20,845
Files
162
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
23
Internal functions
48
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
1.64
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
12
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-12-15
Latest release
2026-05-19
Avg cadence
189 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 23
- Examples that run
- 100%23 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 99%
- Return-value docs
- 100%
- Help pages citing references
- 39%
- bug fix in usage of aggregateAcrossCells function
From NEWS in the release
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/bodenmillergroup/imcrtools on 2026-10-18.
The R CMD check workflow runs on Linux, and on R-devel
GitHub Pages site last deployed 2026-10-06 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| 20210205_CompSlide_NSCLC_TMA_LC_Dy161_1 | data.frame | 20,000 × 10 | No other package |
| 20210205_CompSlide_NSCLC_TMA_LC_Dy162_2 | data.frame | 20,000 × 10 | No other package |
| 20210205_CompSlide_NSCLC_TMA_LC_Dy163_3 | data.frame | 20,000 × 10 | No other package |
| 20210205_CompSlide_NSCLC_TMA_LC_Dy164_4 | data.frame | 20,000 × 10 | No other package |
| 20210305_NE_mockData2_ROI_001_1 | data.frame | 8,961 × 11 | No other package |
| 20210305_NE_mockData2_ROI_002_2 | data.frame | 3,599 × 11 | No other package |
| 20210305_NE_mockData2_ROI_003_3 | data.frame | 2,862 × 11 | No other package |
| Dy161 | data.frame | 100 × 10 | No other package |
| Dy162 | data.frame | 100 × 10 | No other package |
| Dy163 | data.frame | 100 × 10 | No other package |
| Dy164 | data.frame | 100 × 10 | No other package |
| Experiment | – | – | – |
| Image | data.frame | 15 × 177 | No other package |
| Object_relationships | data.frame | 1,484 × 9 | No other package |
| cell | data.frame | 239 × 206 | No other package |
| images | data.frame | 15 × 15 | No other package |
| panel | data.frame | 5 × 7 | No other package |
| var_Image | data.frame | 173 × 9 | No other package |
| var_cell | data.frame | 204 × 9 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (1)
People
- Daniel Schulz contributor maintainer
- Schiller Chiara contributor
- Nils Eling author
- Jana Fischer contributor
- Tobias Hoch contributor
- Lutz Marlene contributor
- Lasse Meyer contributor
- Ibañez Victor contributor
- Vito Zanotelli contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("imcRtools")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41596-023-00881-0.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.