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MANOR

Bioc current

CGH Micro-Array NORmalization

v1.84.0 · Package record · software · GPL-2
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 1.7 · Oct 14, 2005

Current · Requires R 4.6

1.0 In 42 of 49 releases 3.23

Description

Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

106 0 exported

Complexity

4.2 avg / 34 max

Call network

106 nodes / 117 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.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

9,246

Files

71

Compiled share

57.9%

Has compiled src

Yes

Language breakdown

R 1,533 (16.6%)C/C++/src 5,356 (57.9%)Docs 1,333 (14.4%)Vignettes 1,024 (11.1%)

API

Exported functions

45

Internal functions

0

Testing

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

–

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

–

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

2.10

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

42

First release

2005-10-12

Latest release

2026-04-28

Avg cadence

183 days

Cold removal rate

100%

Dep drift

5

LOC over versions

v1.7: 6,650 LOCv1.8: 6,655 LOCv1.9: 6,683 LOCv2.0: 6,759 LOCv2.1: 6,760 LOCv2.2: 6,718 LOCv2.3: 6,557 LOCv2.4: 6,571 LOCv2.5: 6,573 LOCv2.6: 6,560 LOCv2.7: 6,560 LOCv2.8: 6,560 LOCv2.9: 6,560 LOCv2.10: 6,560 LOCv2.11: 6,560 LOCv2.12: 6,560 LOCv2.13: 6,569 LOCv2.14: 9,089 LOCv3.0: 9,006 LOCv3.1: 9,006 LOCv3.2: 9,006 LOCv3.3: 9,006 LOCv3.4: 9,006 LOCv3.5: 9,006 LOCv3.6: 9,006 LOCv3.7: 9,006 LOCv3.8: 9,006 LOCv3.9: 9,006 LOCv3.10: 9,006 LOCv3.11: 9,246 LOCv3.12: 9,246 LOCv3.13: 9,246 LOCv3.14: 9,246 LOCv3.15: 9,246 LOCv3.16: 9,246 LOCv3.17: 9,246 LOCv3.18: 9,246 LOCv3.19: 9,246 LOCv3.20: 9,246 LOCv3.21: 9,246 LOCv3.22: 9,246 LOCv3.23: 9,246 LOC

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

Documentation

In the Bioconductor 3.23 release
READMEYes · 79 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structuredCitation fileNoWebsiteYes
Help pages
19 (1 internal)
Examples that run
100%16 run in a plain check
Exported functions with examples
87%
Documented parameters
not tracked
Return-value docs
not tracked
Help pages citing references
21%
Vignettes (1)
How these are measured

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/pneuvial/manor on 2026-10-21.

Continuous integration (3)
GitHub ActionsR CMD check workflowAppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Coverage (1)
Coverage reporting
How this is detected·Detection ruleset v4 (2026-10-20)

Datasets

Bundled datasets · 33
NameClassSizeAlso in
SNR.flagflag5 elementsNo other package
amplicon.flagflag5 elementsNo other package
chromosome.flagflag5 elementsNo other package
clone.qscoreqscore6 elementsNo other package
control.flagflag5 elementsNo other package
dapi.snr.flagflag5 elementsNo other package
dyn.x.qscoreqscore6 elementsNo other package
dyn.y.qscoreqscore6 elementsNo other package
dynamics.qscoreqscore6 elementsNo other package
edgearrayCGH4 elementsNo other package
edge.normarrayCGH7 elementsNo other package
global.spatial.flagflag5 elementsNo other package
gradientarrayCGH4 elementsNo other package
gradient.normarrayCGH7 elementsNo other package
intensity.flagflag5 elementsNo other package
local.spatial.flagflag5 elementsNo other package
num.chromosome.flagflag5 elementsNo other package
pct.clone.qscoreqscore6 elementsNo other package
pct.replicate.qscoreqscore6 elementsNo other package
pct.spot.before.qscoreqscore6 elementsNo other package
pct.spot.qscoreqscore6 elementsNo other package
position.flagflag5 elementsNo other package
ref.snr.flagflag5 elementsNo other package
rep.flagflag5 elementsNo other package
replicate.aux–––
replicate.flagflag5 elementsNo other package
smoothness.qscoreqscore6 elementsNo other package
spatial.flagflag5 elementsNo other package
spot.corr.flagflag5 elementsNo other package
spot.flagflag5 elementsNo other package
unique.flagflag5 elementsNo other package
val.mark.flagflag5 elementsNo other package
var.replicate.qscoreqscore6 elementsNo other package

All of MANOR's data objects

Topics

Software › Technology › Microarray
Software › Technology › Microarray › TwoChannel
Software › Infrastructure › DataImport
Software › WorkflowStep › QualityControl
Software › WorkflowStep › Preprocessing
Software › AssayDomain › CopyNumberVariation
Software › WorkflowStep › Normalization
Maintainer
Pierre Neuvial

Available on

CRANr2uBioconductorautoCRANCOPR

People (from the free-text Author field)

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MANOR")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for MANOR version 1.84.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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