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dominoSignal

Bioc current

Cell Communication Analysis for Single Cell RNA Sequencing

v1.6.0 · software · GPL-3 | file LICENSE
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.20 · Oct 30, 2024

Current · Requires R 4.6

1.0 In 4 of 49 releases 3.23

Description

dominoSignal is a package developed to analyze cell signaling through ligand - receptor - transcription factor networks in scRNAseq data. It takes as input information transcriptomic data, requiring counts, z-scored counts, and cluster labels, as well as information on transcription factor activation (such as from SCENIC) and a database of ligand and receptor pairings (such as from CellPhoneDB). This package creates an object storing ligand - receptor - transcription factor linkages by cluster and provides several methods for exploring, summarizing, and visualizing the analysis.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

45 33 exported

Complexity

8.2 avg / 42 max

Call network

45 nodes / 19 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

6,940

Files

105

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,300 (47.6%)Tests 521 (7.5%)Docs 2,022 (29.1%)Vignettes 1,097 (15.8%)

API

Exported functions

33

Internal functions

12

Recent export changes

v3.21+2 obtain_circos_expression, render_circos_ligand_receptor
v3.20+31 add_rl_column, build_domino, circos_ligand_receptor +28 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.16

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

0%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2.0

System requirements

–

C++ standard

–

License

GPL-3 | file LICENSE

License flags

SPDX valid, not OSI

History

Versions

4

First release

2024-10-29

Latest release

2026-04-29

Avg cadence

168 days

Cold removal rate

–

Dep drift

3

LOC over versions

v3.20: 5,917 LOCv3.21: 6,506 LOCv3.22: 6,506 LOCv3.23: 6,940 LOC

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

Documentation

Documentation
READMEYes · 433 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
98%
Return-value docs
100%
References docs
0%

Topics

Software › ResearchField › SystemsBiology
Software › Technology › SingleCell
Software › ResearchField › Transcriptomics
Software › WorkflowStep › Visualization › Network

People

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