SpaNorm
Bioc currentSpatially-aware normalisation for spatial transcriptomics data
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
This package implements the spatially aware library size normalisation algorithm, SpaNorm. SpaNorm normalises out library size effects while retaining biology through the modelling of smooth functions for each effect. Normalisation is performed in a gene- and cell-/spot- specific manner, yielding library size adjusted data.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
62 3 exported
Complexity
4.8 avg / 29 max
Call network
62 nodes / 88 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
3,920
Files
41
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
58
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.31
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
181 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
- 11 (1 internal)
- Examples that run
- 100%9 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 9% with a bibliography file
- SpaNorm HTML
Repository practices
6 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/bhuvad/spanorm on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow
Datasets
Topics
People
- Dharmesh D. Bhuva author maintainer
- Ahmed Mohamed author
- Agus Salim author
Cite
Cite this package
Run in R for the authors' entry:
citation("SpaNorm")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/2024.05.31.596908.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.