Skip to content

hipathia

Bioc current

HiPathia: High-throughput Pathway Analysis

v3.12.0 · software · GPL-2
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

Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

133 36 exported

Complexity

3.9 avg / 32 max

Call network

133 nodes / 145 edges

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

Call graph

Open call graph →
Loading call graph…

Lowest coverage

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

Code

Structure

Lines of code

10,078

Files

155

Compiled share

0%

Has compiled src

No

Language breakdown

R 6,104 (60.6%)Tests 490 (4.9%)Docs 2,424 (24.1%)Vignettes 1,060 (10.5%)

API

Exported functions

36

Internal functions

96

Recent export changes

v3.9+4 get_go_names, get_node_names, get_nodes_data +1 more
v3.8+1 top_pathways

Testing & CI

Has tests

Yes

Test-to-code ratio

0.08

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

17.4%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

17

First release

2018-04-30

Latest release

2026-04-28

Avg cadence

183 days

Cold removal rate

100%

Dep drift

9

LOC over versions

v3.7: 6,948 LOCv3.8: 7,024 LOCv3.9: 7,421 LOCv3.10: 8,374 LOCv3.11: 8,281 LOCv3.12: 8,281 LOCv3.13: 8,281 LOCv3.14: 8,281 LOCv3.15: 8,374 LOCv3.16: 8,389 LOCv3.17: 10,262 LOCv3.18: 10,041 LOCv3.19: 10,041 LOCv3.20: 10,041 LOCv3.21: 10,041 LOCv3.22: 10,074 LOCv3.23: 10,078 LOC

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

Documentation

Documentation
READMEYes · 83 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
0%

Topics

Software › WorkflowStep › Pathways
Software › StatisticalMethod › GraphAndNetwork
Software › AssayDomain › GeneExpression
Software › BiologicalQuestion › GeneSignaling
Software › WorkflowStep › Pathways › GO

People

Report a problem with this page →