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rGREAT

Bioc current

GREAT Analysis - Functional Enrichment on Genomic Regions

v2.14.0 · software · MIT + file LICENSE
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Release Lineage

Entered 3.1 · Apr 17, 2015

Current · Requires R 4.6

1.0 In 23 of 49 releases 3.23

Description

GREAT (Genomic Regions Enrichment of Annotations Tool) is a type of functional enrichment analysis directly performed on genomic regions. This package implements the GREAT algorithm (the local GREAT analysis), also it supports directly interacting with the GREAT web service (the online GREAT analysis). Both analysis can be viewed by a Shiny application. rGREAT by default supports more than 600 organisms and a large number of gene set collections, as well as self-provided gene sets and organisms from users. Additionally, it implements a general method for dealing with background regions.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

56 22 exported

Complexity

8.8 avg / 87 max

Call network

56 nodes / 85 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

37,555

Files

256

Compiled share

0.2%

Has compiled src

Yes

Language breakdown

R 5,031 (13.4%)C/C++/src 70 (0.2%)Tests 259 (0.7%)Docs 1,487 (4%)Vignettes 30,708 (81.8%)

API

Exported functions

22

Internal functions

30

Recent export changes

v3.9+1 GreatJob

Testing & CI

Has tests

Yes

Test-to-code ratio

0.05

testthat edition

–

CI present

Yes

CI type

["github-actions","travis"]

PR gated

Yes

Docs

Roxygen coverage

90.9%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

38.5%

Unsafe pattern score

3

Dep constraint coverage

3.7%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

–

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

23

First release

2015-04-16

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

21

LOC over versions

v3.1: 1,551 LOCv3.2: 1,550 LOCv3.3: 1,636 LOCv3.4: 1,709 LOCv3.5: 1,712 LOCv3.6: 1,780 LOCv3.7: 1,780 LOCv3.8: 1,784 LOCv3.9: 1,787 LOCv3.10: 1,797 LOCv3.11: 2,012 LOCv3.12: 2,028 LOCv3.13: 2,028 LOCv3.14: 2,028 LOCv3.15: 2,028 LOCv3.16: 7,234 LOCv3.17: 7,733 LOCv3.18: 7,733 LOCv3.19: 37,566 LOCv3.20: 37,566 LOCv3.21: 37,555 LOCv3.22: 37,555 LOCv3.23: 37,555 LOC

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

Documentation

Documentation
READMEYes · 188 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 33% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
98%
Return-value docs
85%
References docs
0%

Topics

Software › BiologicalQuestion › GeneSetEnrichment
Software › WorkflowStep › Pathways › GO
Software › WorkflowStep › Pathways
Software
Software › Technology › Sequencing
Software › Technology › Sequencing › WholeGenome
Software › BiologicalQuestion › GenomeAnnotation
Software › BiologicalQuestion › Coverage

Depended on by (3)

Bioconductor (3)

profileplyr ATACCoGAPS HMMRATAC

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