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phantasus

Bioc current

Visual and interactive gene expression analysis

v1.32.0 · software · MIT + file LICENSE
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.7 · May 1, 2018

Current · Requires R 4.6

1.0 In 17 of 49 releases 3.23

Description

Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

104 10 exported

Complexity

4.8 avg / 19 max

Call network

104 nodes / 123 edges

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

Call graph

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Lowest coverage

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

Code

Structure

Lines of code

6,245

Files

243

Compiled share

0%

Has compiled src

No

Language breakdown

R 3,914 (62.7%)Tests 591 (9.5%)Docs 1,239 (19.8%)Vignettes 501 (8%)

API

Exported functions

10

Internal functions

94

Recent export changes

v3.7+7 getES, getGDS, getGSE +4 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.15

testthat edition

–

CI present

Yes

CI type

["travis","appveyor"]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

7.1%

Unsafe pattern score

2

Dep constraint coverage

7.9%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.3

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

17

First release

2018-07-22

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

–

Dep drift

25

LOC over versions

v3.7: 2,862 LOCv3.8: 3,470 LOCv3.9: 3,680 LOCv3.10: 3,680 LOCv3.11: 4,339 LOCv3.12: 4,431 LOCv3.13: 4,431 LOCv3.14: 4,431 LOCv3.15: 5,090 LOCv3.16: 5,146 LOCv3.17: 5,146 LOCv3.18: 5,493 LOCv3.19: 6,133 LOCv3.20: 6,101 LOCv3.21: 6,101 LOCv3.22: 6,101 LOCv3.23: 6,245 LOC

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

Documentation

Documentation
READMEYes · 328 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo
Examples that run
11%
Documented parameters
92%
Return-value docs
80%
References docs
0%

Topics

Software › AssayDomain › GeneExpression
Software › Infrastructure › GUI
Software › WorkflowStep › Visualization
Software › Infrastructure › DataRepresentation
Software › ResearchField › Transcriptomics
Software › Technology › Sequencing › RNASeq
Software › Technology › Microarray
Software › WorkflowStep › Normalization
Software › StatisticalMethod › Clustering
Software › BiologicalQuestion › DifferentialExpression
Software › StatisticalMethod › PrincipalComponent
Software › ResearchField › Immunology › ImmunoOncology

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