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qsea

Bioc current

IP-seq data analysis and vizualization

v1.38.0 · software · GPL-2
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.4 · Oct 18, 2016

Current · Requires R 4.6

1.0 In 20 of 49 releases 3.23

Description

qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

52 21 exported

Complexity

10.3 avg / 60 max

Call network

52 nodes / 58 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

5,672

Files

46

Compiled share

2.2%

Has compiled src

Yes

Language breakdown

R 3,333 (58.8%)C/C++/src 123 (2.2%)Tests 45 (0.8%)Docs 1,349 (23.8%)Vignettes 822 (14.5%)

API

Exported functions

21

Internal functions

29

Recent export changes

v3.5+1 addNewSamples

Testing & CI

Has tests

Yes

Test-to-code ratio

0.01

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

4.3

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

20

First release

2016-12-05

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

7

LOC over versions

v3.4: 5,356 LOCv3.5: 5,616 LOCv3.6: 5,636 LOCv3.7: 5,639 LOCv3.8: 5,644 LOCv3.9: 5,644 LOCv3.10: 5,650 LOCv3.11: 5,650 LOCv3.12: 5,650 LOCv3.13: 5,652 LOCv3.14: 5,652 LOCv3.15: 5,672 LOCv3.16: 5,672 LOCv3.17: 5,672 LOCv3.18: 5,672 LOCv3.19: 5,672 LOCv3.20: 5,672 LOCv3.21: 5,672 LOCv3.22: 5,672 LOCv3.23: 5,672 LOC

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

Documentation

Documentation
READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
94%
Return-value docs
100%
References docs
4%

Topics

Software › Technology › Sequencing
Software › AssayDomain › DNAMethylation
Software › AssayDomain › CpGIsland
Software › Technology › Sequencing › ChIPSeq
Software › WorkflowStep › Preprocessing
Software › WorkflowStep › Normalization
Software › WorkflowStep › QualityControl
Software › WorkflowStep › Visualization
Software › AssayDomain › CopyNumberVariation
Software › Technology › Microarray › ChipOnChip
Software › BiologicalQuestion › DifferentialMethylation

Depended on by (2)

Bioconductor (2)

MEDIPSData mesa

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