Package: Harshlight 1.79.0

Maurizio Pellegrino

Harshlight: A "corrective make-up" program for microarray chips

The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.

Authors:Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkowski, Marcelo O. Magnasco

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Harshlight.pdf |Harshlight.html✨
Harshlight/json (API)

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

Peer review:

Datasets:
  • sim - Blemish simulations from 100.000 random chips
  • sim.int - Blemish simulations from 100.000 random chips

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

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarrayqualitycontrolpreprocessingonechannelreportwriting

4.20 score 2 scripts 364 downloads 8 mentions 3 exports 28 dependencies

Last updated 26 days agofrom:ed62604b49. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-win-x86_64WARNINGNov 20 2024
R-4.5-linux-x86_64WARNINGNov 20 2024
R-4.4-win-x86_64WARNINGNov 20 2024
R-4.4-mac-x86_64WARNINGNov 20 2024
R-4.4-mac-aarch64WARNINGNov 20 2024
R-4.3-win-x86_64WARNINGNov 20 2024
R-4.3-mac-x86_64WARNINGNov 20 2024
R-4.3-mac-aarch64WARNINGNov 20 2024

Exports:HarshCompHarshExtHarshlight

Dependencies:affyaffyioaltcdfenvsaskpassBiobaseBiocGenericsBiocManagerBiostringscrayoncurlgenericsGenomeInfoDbGenomeInfoDbDatagraphhttrhypergraphIRangesjsonlitemakecdfenvmimeopensslpreprocessCoreR6S4VectorssysUCSC.utilsXVectorzlibbioc

Harshlight

Rendered fromHarshlight.Rnwusingutils::Sweaveon Nov 20 2024.

Last update: 2013-11-01
Started: 2013-11-01