scider
Bioc currentSpatial cell-type inter-correlation by density in R
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
scider is an user-friendly R package providing functions to model the global density of cells in a slide of spatial transcriptomics data. All functions in the package are built based on the SpatialExperiment object, allowing integration into various spatial transcriptomics-related packages from Bioconductor. After modelling density, the package allows for several downstream analysis, including colocalization analysis, boundary detection analysis and differential density analysis.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
84 43 exported
Complexity
7.1 avg / 31 max
Call network
84 nodes / 80 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
9,188
Files
143
Compiled share
7.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
43
Internal functions
28
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
3
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-10-24
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
13
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
- 97%
- Return-value docs
- 80%
- References docs
- 0%
Topics
Depended on by (1)
Bioconductor (1)
People
- Yunshun Chen author maintainer
- Mengbo Li author
- Ning Liu author
- Quoc Hoang Nguyen author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("scider")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.