MoleculeExperiment
Bioc currentPrioritising a molecule-level storage of Spatial Transcriptomics Data
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
MoleculeExperiment contains functions to create and work with objects from the new MoleculeExperiment class. We introduce this class for analysing molecule-based spatial transcriptomics data (e.g., Xenium by 10X, Cosmx SMI by Nanostring, and Merscope by Vizgen). This allows researchers to analyse spatial transcriptomics data at the molecule level, and to have standardised data formats accross vendors.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
32 15 exported
Complexity
4.1 avg / 14 max
Call network
32 nodes / 46 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
4,481
Files
76
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
17
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.25
testthat edition
3
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
5.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
2.10
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-10-09
Latest release
2026-04-28
Avg cadence
175 days
Cold removal rate
100%
Dep drift
1
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
Depended on by (1)
Bioconductor (1)
People
- Shila Ghazanfar author maintainer
- Ellis Patrick author
- Bárbara Zita Peters Couto author
- Nicholas Robertson author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("MoleculeExperiment")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.