Package: NormalyzerDE 1.23.0
NormalyzerDE: Evaluation of normalization methods and calculation of differential expression analysis statistics
NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.
Authors:
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NEWS
# Install 'NormalyzerDE' in R: |
install.packages('NormalyzerDE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/computationalproteomics/normalyzerde/issues
On BioConductor:NormalyzerDE-1.23.0(bioc 3.20)NormalyzerDE-1.22.0(bioc 3.19)
Last updated 2 months agofrom:861595f37e
Exports:analyzeNormalizationscalculateContrastsgenerateAnnotatedMatrixgeneratePlotsgenerateStatsReportgetRTNormalizedMatrixgetSmoothedRTNormalizedMatrixgetVerifiedNormalyzerObjectglobalIntensityNormalizationmeanNormalizationmedianNormalizationnormalyzernormalyzerDENormalyzerEvaluationResultsNormalyzerResultsNormalyzerStatisticsnormMethodsperformCyclicLoessNormalizationperformGlobalRLRNormalizationperformQuantileNormalizationperformSMADNormalizationperformVSNNormalizationreduceTechnicalReplicatessetupJobDirsetupRawContrastObjectsetupRawDataObjectsetupTestDatawriteNormalizedDatasets
Dependencies:abindaffyaffyioapeaskpassbackportsBiobaseBiocGenericsBiocManagerbootbriobroomcallrcarcarDataclicolorspacecpp11crayoncurlDelayedArraydescdiffobjdigestdplyrevaluatefansifarverfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggforceggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclelimmalme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmgcvmimeminqamunsellnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgbuildpkgconfigpkgloadpolyclippraisepreprocessCoreprocessxpspurrrquantregR6RColorBrewerRcppRcppEigenrematch2rlangrprojrootS4ArraysS4VectorsscalesSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstestthattibbletidyrtidyselecttweenrUCSC.utilsutf8vctrsviridisLitevsnwaldowithrXVectorzlibbioc