Package: PREDA
Version: 1.58.0
Title: Position Related Data Analysis
Author: Francesco Ferrari <francesco.ferrari@ifom.eu>
Maintainer: Francesco Ferrari <francesco.ferrari@ifom.eu>
License: GPL-2
Depends: R (>= 2.9.0), Biobase, lokern (>= 1.0.9), multtest, stats,
        methods, annotate
Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata
Enhances: Rmpi, rsprng
Description: Package for the position related analysis of quantitative
        functional genomics data.
Collate: AllClasses.R AllGenerics.R analysesNames.R
        CleanNAAnnotationDataframe.R
        compareFunctionFromStatisticsForPREDA.R
        computeDatasetSignature.R DataForPREDA2dataframe.R
        DataForPREDA2GenomicAnnotationsForPREDA.R
        DataForPREDA2StatisticsForPREDA.R datasetSignatureFromFlags.R
        eset2GenomicAnnotations.R GE_computeStatistic.R
        GEhighWeakExpressionWorkflow.R genomePlot_improved.R
        genomePlot.R GenomicAnnotations2dataframe.R
        GenomicAnnotations2GenomicAnnotationsForPREDA.R
        GenomicAnnotations2reference_positions.R
        GenomicAnnotationsExtract.R GenomicAnnotationsFilter_neg.R
        GenomicAnnotationsFilter_pos.R
        GenomicAnnotationsForPREDA2dataframe.R
        GenomicAnnotationsForPREDA2GenomicAnnotations.R
        GenomicAnnotationsForPREDA2PREDAResults.R
        GenomicAnnotationsForPREDAFromfile.R
        GenomicAnnotationsForPREDAGetExpectedFlags.R
        GenomicAnnotationsFromdataframe.R GenomicAnnotationsFromfile.R
        GenomicAnnotationsFromLibrary.R
        GenomicAnnotationsSortAndCleanNA.R GenomicRegions2dataframe.R
        GenomicRegionsAnnotate.R GenomicRegionsChrNumber.R
        GenomicRegionsComparison.R GenomicRegionsCreateRegionsIds.R
        GenomicRegionsFilter_neg.R GenomicRegionsFilter_pos.R
        GenomicRegionsFindOverlap.R GenomicRegionsFromdataframe.R
        GenomicRegionsFromfile.R GenomicRegionsNumber.R
        GenomicRegionsSpan.R GenomicRegionsTotalSpan.R
        GEsimulationsWorkflow.R getExpectedSmoothFunction.R
        getExpectedSmoothFunction_runmean.R getObservedSmoothFunction.R
        getObservedSmoothFunction_runmean.R getStatisticByName.R
        initialize-methods.R MergeStatisticAnnotations2DataForPREDA.R
        PREDADataAndResults2dataframe.R PREDA_main_permRows.R
        PREDA_main_permSamples.R PREDA_main.R
        PREDA_multTestCorrection.R PREDA_quantsmoothStatPerm.R
        PREDA_quantsmoothStat.R PREDAResults2dataframe.R
        PREDAResults2GenomicRegions.R
        PREDAResults2GenomicRegionsSingle.R
        PREDAResults2PREDADataAndResults.R
        PREDAResultsGetObservedFlags.R PREDA_smoothStatPerm.R
        PREDA_smoothStat.R PREDA_splineStatPerm.R PREDA_splineStat.R
        preprocessingGE.R RMAwithCDFfilter.R simulations.R
        SODEGIR_GEstatistics.R SODEGIRpreprocessingGE.R
        SortAnnotationDataframe.R StatisticsForPREDA2dataframe.R
        StatisticsForPREDAFilterColumns_neg.R
        StatisticsForPREDAFilterColumns_pos.R
        StatisticsForPREDAFromdataframe.R statisticsForPREDAfromEset.R
        StatisticsForPREDAFromfile.R
biocViews: Software, CopyNumberVariation, GeneExpression, Genetics
Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:35:39 UTC
RemoteUrl: https://github.com/bioc/PREDA
RemoteRef: RELEASE_3_23
RemoteSha: cffa80d28c1ea191f2655a9f25f8dedadaedfa4e
NeedsCompilation: no
Packaged: 2026-04-29 23:57:26 UTC; root
Built: R 4.6.0; ; 2026-04-29 23:59:48 UTC; windows
