DESpace

Bioc current

DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions

v2.4.0 · software · GPL-3

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Release Lineage

Entered 3.17 · Apr 26, 2023

Current · Requires R 4.6

1.0 In 7 of 49 releases 3.23

Description

Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

36 6 exported

Complexity

4.7 avg / 22 max

Call network

36 nodes / 30 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

4,282

Files

Compiled share

Has compiled src

Language breakdown

R 2,161 (50.5%)Tests 110 (2.6%)Docs 783 (18.3%)Vignettes 1,228 (28.7%)

API

Exported functions

Internal functions

Recent export changes

v3.21+4 dsp_test, individual_dsp, individual_svg +1 more −2 DESpace_test, individual_test

Testing & CI

Has tests

Yes

Test-to-code ratio

0.05

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

Dep constraint coverage

Secret pattern count

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

First release

2023-10-10

Latest release

2026-04-28

Avg cadence

128 days

Cold removal rate

100%

Dep drift

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 238 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Topics

Software › Technology › Spatial

Software › Technology › SingleCell

Software › Technology › Sequencing › RNASeq

Software › ResearchField › Transcriptomics

Software › AssayDomain › GeneExpression

Software › Technology › Sequencing

Software › BiologicalQuestion › DifferentialExpression

Software › StatisticalMethod

Software › WorkflowStep › Visualization

Depended on by (1)

Bioconductor (1)

OSTA

People

Peiying Cai author maintainer
Simone Tiberi author

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