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TFEA.ChIP

Bioc current

TFEA.ChIP, a Tool Kit for Transcription Factor Enrichment

v1.32.0 · software · Artistic-2.0
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

Package to analyze transcription factor enrichment in a gene set using data from ChIP-Seq experiments.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

22 21 exported

Complexity

7 avg / 23 max

Call network

22 nodes / 18 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

3,719

Files

69

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,245 (60.4%)Docs 1,091 (29.3%)Vignettes 383 (10.3%)

API

Exported functions

21

Internal functions

1

Recent export changes

v3.9+1 rankTFs
v3.7+15 GR2tfbs_db, GSEA_EnrichmentScore, GSEA_run +12 more

Testing & CI

Has tests

No

Test-to-code ratio

0.00

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

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

17

First release

2018-04-30

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

5

LOC over versions

v3.7: 3,013 LOCv3.8: 3,086 LOCv3.9: 3,396 LOCv3.10: 3,395 LOCv3.11: 3,395 LOCv3.12: 3,395 LOCv3.13: 3,353 LOCv3.14: 3,353 LOCv3.15: 3,275 LOCv3.16: 3,275 LOCv3.17: 3,275 LOCv3.18: 3,275 LOCv3.19: 3,275 LOCv3.20: 3,275 LOCv3.21: 3,275 LOCv3.22: 3,719 LOCv3.23: 3,719 LOC

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

Documentation

Documentation
READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
100%
Return-value docs
100%
References docs
0%

Topics

Software › AssayDomain › Transcription
Software › BiologicalQuestion › GeneRegulation
Software › BiologicalQuestion › GeneSetEnrichment
Software › ResearchField › Transcriptomics
Software › Technology › Sequencing
Software › Technology › Sequencing › ChIPSeq
Software › Technology › Sequencing › RNASeq
Software › ResearchField › Immunology › ImmunoOncology
Software › AssayDomain › GeneExpression
Software › Technology › Microarray › ChipOnChip

Depended on by (1)

Bioconductor (1)

ChIPDBData

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