MPAC

Bioc current

Multi-omic Pathway Analysis of Cells

v1.6.0 · software · GPL-3

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Release Lineage

Entered 3.20 · Oct 30, 2024

Current · Requires R 4.6

1.0 In 4 of 49 releases 3.23

Description

Multi-omic Pathway Analysis of Cells (MPAC), integrates multi-omic data for understanding cellular mechanisms. It predicts novel patient groups with distinct pathway profiles as well as identifying key pathway proteins with potential clinical associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA states (i.e., repressed, normal, or activated), which serve as the input for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes DNA and RNA states to create a background distribution to filter IPLs as a way to remove events observed by chance. It provides multiple methods for downstream analysis and visualization.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

45 20 exported

Complexity

1.6 avg / 6 max

Call network

45 nodes / 31 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

3,330

Files

117

Compiled share

Has compiled src

Language breakdown

R 1,496 (44.9%)Tests 428 (12.9%)Docs 803 (24.1%)Vignettes 603 (18.1%)

API

Exported functions

Internal functions

Recent export changes

v3.21+6 getSignifOvrOnCl, pltConMtf, pltMtfPrtIPL +3 more

v3.20+14 clSamp, colPermIPL, colRealIPL +11 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.29

testthat edition

CI present

CI type

[]

PR gated

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

Unsafe pattern score

Dep constraint coverage

90.9%

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4.0

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

First release

2024-10-29

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

–

Dep drift

LOC over versions

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

Documentation

READMEYes · 239 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Topics

Software

Software › Technology

Software › Technology › Sequencing

Software › Technology › Sequencing › RNASeq

Software › StatisticalMethod › Survival

Software › StatisticalMethod › Clustering

Software › ResearchField › Immunology › ImmunoOncology

People

Peng Liu author maintainer
Paul Ahlquist author
Anthony Gitter author
Irene Ong author

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