standR
Bioc currentSpatial transcriptome analyses of Nanostring's DSP data in R
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. standR allows data inspection, quality control, normalization, batch correction and evaluation with informative visualizations.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
43 17 exported
Complexity
2.7 avg / 13 max
Call network
43 nodes / 41 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
3,965
Files
62
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
21
Internal functions
26
Testing
Has tests
Yes
Test-to-code ratio
0.20
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
4.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 23 (2 internal)includes a package overview page
- Examples that run
- 100%22 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 9%
- standR_introduction HTML
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/davislaboratory/standr on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2022-04-09 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| dkd_spe_subset | – | – | – |
| metadata | data.frame | 3 × 17 | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People
- Ning Liu author maintainer
- Dharmesh D Bhuva author
- Ahmed Mohamed author
Cite
Cite this package
Run in R for the authors' entry:
citation("standR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/nar/gkad1026.
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.