jazzPanda
Bioc currentFinding spatially relevant marker genes in image based spatial transcriptomics data
Release Lineage
Entered 3.21 · Apr 16, 2025
Current · Requires R 4.6
Description
This package contains the function to find marker genes for image-based spatial transcriptomics data. There are functions to create spatial vectors from the cell and transcript coordiantes, which are passed as inputs to find marker genes. Marker genes are detected for every cluster by two approaches. The first approach is by permtuation testing, which is implmented in parallel for finding marker genes for one sample study. The other approach is to build a linear model for every gene. This approach can account for multiple samples and backgound noise.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
21 9 exported
Complexity
5.4 avg / 18 max
Call network
21 nodes / 14 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
6,733
Files
56
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
12
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.73
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2025-08-22
Latest release
2026-04-28
Avg cadence
125 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 28includes a package overview page
- 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
- 0%
- jazzPanda example HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/phipsonlab/jazzpanda on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-09-03 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| rep1_clusters | data.frame | 1,705 × 6 | No other package |
| rep1_neg | – | – | – |
| rep1_sub | – | – | – |
| rep2_clusters | data.frame | 1,815 × 6 | No other package |
| rep2_neg | – | – | – |
| rep2_sub | – | – | – |
Topics
People
- Melody Jin author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("jazzPanda")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
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