Package: MANOR 1.79.0

Pierre Neuvial

MANOR: CGH Micro-Array NORmalization

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

Authors:Pierre Neuvial <[email protected]>, Philippe Hupé <[email protected]>

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MANOR/json (API)
NEWS

# Install 'MANOR' in R:
install.packages('MANOR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pneuvial/manor/issues

Datasets:
  • SNR.flag - Examples of flag objects to apply to CGH arrays
  • amplicon.flag - Examples of flag objects to apply to CGH arrays
  • chromosome.flag - Examples of flag objects to apply to CGH arrays
  • clone.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • control.flag - Examples of flag objects to apply to CGH arrays
  • dapi.snr.flag - Examples of flag objects to apply to CGH arrays
  • dyn.x.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • dyn.y.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • dynamics.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • edge - Examples of array-CGH data with spatial artifacts
  • edge.norm - Examples of array-CGH data with spatial artifacts
  • global.spatial.flag - Examples of flag objects to apply to CGH arrays
  • gradient - Examples of array-CGH data with spatial artifacts
  • gradient.norm - Examples of array-CGH data with spatial artifacts
  • intensity.flag - Examples of flag objects to apply to CGH arrays
  • local.spatial.flag - Examples of flag objects to apply to CGH arrays
  • pct.clone.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • pct.replicate.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • pct.spot.before.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • pct.spot.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • position.flag - Examples of flag objects to apply to CGH arrays
  • ref.snr.flag - Examples of flag objects to apply to CGH arrays
  • rep.flag - Examples of flag objects to apply to CGH arrays
  • replicate.flag - Examples of flag objects to apply to CGH arrays
  • smoothness.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays
  • spatial.flag - Examples of flag objects to apply to CGH arrays
  • spot.flag - Examples of flag objects to apply to CGH arrays
  • unique.flag - Examples of flag objects to apply to CGH arrays
  • val.mark.flag - Examples of flag objects to apply to CGH arrays
  • var.replicate.qscore - Examples of qscore objects (quality scores) to apply to CGH arrays

On BioConductor:MANOR-1.79.0(bioc 3.21)MANOR-1.78.0(bioc 3.20)

microarraytwochanneldataimportqualitycontrolpreprocessingcopynumbervariationnormalization

5.10 score 1 scripts 390 downloads 7 mentions 45 exports 4 dependencies

Last updated 2 months agofrom:8992a9b522. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesFAILDec 18 2024
R-4.5-win-x86_64WARNINGDec 18 2024
R-4.5-linux-x86_64WARNINGDec 18 2024
R-4.4-win-x86_64WARNINGDec 18 2024
R-4.4-mac-x86_64WARNINGDec 18 2024
R-4.4-mac-aarch64WARNINGDec 18 2024
R-4.3-win-x86_64WARNINGDec 18 2024
R-4.3-mac-x86_64WARNINGDec 18 2024
R-4.3-mac-aarch64WARNINGDec 18 2024

Exports:add.linesarrayCGH2txtarrayTrendarrayTrend.arrayCGHarrayTrend.defaultcentercheck.nameschromcvdetectSBdetectSB.arrayCGHflag.aggregate.arrayCGHflag.arrayCGHflag.summaryflag.summary.arrayCGHflag.summary.defaultgenome.plotgenome.plot.arrayCGHgenome.plot.defaultgetChromosomeArmhtml.reporthtml.report.arrayCGHhtml.report.defaultimportimport.default.auximport.gpr.auximport.spot.auxintensity.plotmy.aggregate.data.framenemnem.arrayCGHnem.defaultnormnorm.arrayCGHprint.flagqscore.arrayCGHqscore.summary.arrayCGHrenamereport.plotreport.plot.arrayCGHreport.plot.defaultsort.arrayCGHto.flagto.qscorew

Dependencies:awsawsMethodsGLADgsl

Readme and manuals

Help Manual

Help pageTopics
Spatial trend of microarray spots statisticarrayTrend arrayTrend.arrayCGH arrayTrend.default
Spatial bias detectiondetectSB detectSB.arrayCGH detectSB.default
Apply a flag to an arrayCGHflag flag.arrayCGH
Summarize information about flags after array normalizationflag.summary flag.summary.arrayCGH flag.summary.default
Examples of flag objects to apply to CGH arraysamplicon.flag chromosome.flag control.flag dapi.snr.flag flags global.spatial.flag intensity.flag local.spatial.flag position.flag ref.snr.flag rep.flag replicate.flag SNR.flag spatial.flag spot.flag unique.flag val.mark.flag
Pan-genomic representation of a normalized arrayCGHgenome.plot genome.plot.arrayCGH genome.plot.default
Generate an HTML report of array normalizationhtml.report html.report.arrayCGH html.report.default
Import raw file to an arrayCGH objectimport import.default.aux import.gpr.aux import.spot.aux
Spatial Classification by EM algorithmnem nem.arrayCGH nem.default
Normalize an object of type arrayCGHMANOR manor norm norm.arrayCGH
Create an object of type qscoreqscore to.qscore
arrayCGH quality scoreqscore.arrayCGH
Compute quality scores for a given arrayCGH objectqscore.summary qscore.summary.arrayCGH
Examples of qscore objects (quality scores) to apply to CGH arraysclone.qscore dyn.x.qscore dyn.y.qscore dynamics.qscore pct.clone.qscore pct.replicate.qscore pct.spot.before.qscore pct.spot.qscore smoothness.qscore var.replicate.qscore
Array image and a genomic representation of a normalized arrayCGHreport.plot report.plot.arrayCGH report.plot.default
Sorting for normalized arrayCGH objectssort sort.arrayCGH
Examples of array-CGH data with spatial artifactsedge edge.norm edge.txt gradient gradient.gpr gradient.norm spatial
Create an object of type flagto.flag