SPOTlight
Bioc current`SPOTlight`: Spatial Transcriptomics Deconvolution
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
`SPOTlight` provides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
50 11 exported
Complexity
2.9 avg / 15 max
Call network
50 nodes / 53 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
4,523
Files
48
Compiled share
6.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
11
Internal functions
18
Testing & CI
Has tests
Yes
Test-to-code ratio
0.76
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
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
C++11
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-04-26
Latest release
2026-04-28
Avg cadence
184 days
Cold removal rate
–
Dep drift
4
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
- 79%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Marc Elosua-Bayes author maintainer
- Helena L. Crowell author
- Zachary DeBruine author