Package: SCAN.UPC 2.47.0
Stephen R. Piccolo
SCAN.UPC: Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.
Authors:
SCAN.UPC_2.47.0.tar.gz
SCAN.UPC_2.47.0.zip(r-4.5)SCAN.UPC_2.47.0.zip(r-4.4)SCAN.UPC_2.47.0.zip(r-4.3)
SCAN.UPC_2.47.0.tgz(r-4.4-any)SCAN.UPC_2.47.0.tgz(r-4.3-any)
SCAN.UPC_2.47.0.tar.gz(r-4.5-noble)SCAN.UPC_2.47.0.tar.gz(r-4.4-noble)
SCAN.UPC_2.47.0.tgz(r-4.4-emscripten)SCAN.UPC_2.47.0.tgz(r-4.3-emscripten)
SCAN.UPC.pdf |SCAN.UPC.html✨
SCAN.UPC/json (API)
NEWS
| # Install 'SCAN.UPC' in R: |
| install.packages('SCAN.UPC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SCAN.UPC-2.47.0(bioc 3.20)SCAN.UPC-2.46.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:fee46f764d
Exports:BatchAdjustBatchAdjustFromFileInstallBrainArrayPackageParseMetaFromGtfFileSCANSCAN_TwoColorSCANfastUPCUPC_GenericUPC_Generic_ExpressionSetUPC_RNASeqUPC_RNASeq_SingleUPC_TwoColorUPCfast
Dependencies:abindaffxparseraffyaffyioannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocManagerBiocParallelBiostringsbitbit64blobcachemclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArraydplyredgeRfansifastmapffforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOquerygluehmshttrIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeoligooligoClassesopensslpillarpkgconfigplogrpngpreprocessCoreprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6RcppreadrrlangRSQLiteS4ArraysS4VectorssnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2xtableXVectorzlibbioc
