retrofit
Bioc currentRETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
RETROFIT is a Bayesian non-negative matrix factorization framework to decompose cell type mixtures in ST data without using external single-cell expression references. RETROFIT outperforms existing reference-based methods in estimating cell type proportions and reconstructing gene expressions in simulations with varying spot size and sample heterogeneity, irrespective of the quality or availability of the single-cell reference. RETROFIT recapitulates known cell-type localization patterns in a Slide-seq dataset of mouse cerebellum without using any single-cell data.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 4 exported
Complexity
4.7 avg / 20 max
Call network
38 nodes / 19 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
3,039
Files
44
Compiled share
20.4%
Has compiled src
Yes
Language breakdown
API
Exported functions
4
Internal functions
11
Testing & CI
Has tests
Yes
Test-to-code ratio
1.13
testthat edition
–
CI present
No
CI type
[]
PR gated
No
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
4.2
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-04-25
Latest release
2026-04-28
Avg cadence
182 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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Adam Park author maintainer
- Qunhua Li author
- Roopali Singh author
- Xiang Zhu author