CTSV
Bioc currentIdentification of cell-type-specific spatially variable genes accounting for excess zeros
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
3 2 exported
Complexity
9.7 avg / 22 max
Call network
3 nodes / 0 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
558
Files
14
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
1
Testing & CI
Has tests
Yes
Test-to-code ratio
0.38
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
8
First release
2022-11-01
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
- 67%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Jinge Yu Developer author maintainer
- Xiangyu Luo Developer author