{ "_id": "6a1ab1d31d7bb097a09d5ab6", "Package": "PREDA", "Version": "1.59.0", "Title": "Position Related Data Analysis", "Author": "Francesco Ferrari ", "Maintainer": "Francesco Ferrari ", "License": "GPL-2", "Description": "Package for the position related analysis of quantitative\nfunctional genomics data.", "Collate": "AllClasses.R AllGenerics.R analysesNames.R\nCleanNAAnnotationDataframe.R\ncompareFunctionFromStatisticsForPREDA.R\ncomputeDatasetSignature.R DataForPREDA2dataframe.R\nDataForPREDA2GenomicAnnotationsForPREDA.R\nDataForPREDA2StatisticsForPREDA.R datasetSignatureFromFlags.R\neset2GenomicAnnotations.R GE_computeStatistic.R\nGEhighWeakExpressionWorkflow.R genomePlot_improved.R\ngenomePlot.R GenomicAnnotations2dataframe.R\nGenomicAnnotations2GenomicAnnotationsForPREDA.R\nGenomicAnnotations2reference_positions.R\nGenomicAnnotationsExtract.R GenomicAnnotationsFilter_neg.R\nGenomicAnnotationsFilter_pos.R\nGenomicAnnotationsForPREDA2dataframe.R\nGenomicAnnotationsForPREDA2GenomicAnnotations.R\nGenomicAnnotationsForPREDA2PREDAResults.R\nGenomicAnnotationsForPREDAFromfile.R\nGenomicAnnotationsForPREDAGetExpectedFlags.R\nGenomicAnnotationsFromdataframe.R GenomicAnnotationsFromfile.R\nGenomicAnnotationsFromLibrary.R\nGenomicAnnotationsSortAndCleanNA.R GenomicRegions2dataframe.R\nGenomicRegionsAnnotate.R GenomicRegionsChrNumber.R\nGenomicRegionsComparison.R GenomicRegionsCreateRegionsIds.R\nGenomicRegionsFilter_neg.R GenomicRegionsFilter_pos.R\nGenomicRegionsFindOverlap.R GenomicRegionsFromdataframe.R\nGenomicRegionsFromfile.R GenomicRegionsNumber.R\nGenomicRegionsSpan.R GenomicRegionsTotalSpan.R\nGEsimulationsWorkflow.R getExpectedSmoothFunction.R\ngetExpectedSmoothFunction_runmean.R getObservedSmoothFunction.R\ngetObservedSmoothFunction_runmean.R getStatisticByName.R\ninitialize-methods.R MergeStatisticAnnotations2DataForPREDA.R\nPREDADataAndResults2dataframe.R PREDA_main_permRows.R\nPREDA_main_permSamples.R PREDA_main.R\nPREDA_multTestCorrection.R PREDA_quantsmoothStatPerm.R\nPREDA_quantsmoothStat.R PREDAResults2dataframe.R\nPREDAResults2GenomicRegions.R\nPREDAResults2GenomicRegionsSingle.R\nPREDAResults2PREDADataAndResults.R\nPREDAResultsGetObservedFlags.R PREDA_smoothStatPerm.R\nPREDA_smoothStat.R PREDA_splineStatPerm.R PREDA_splineStat.R\npreprocessingGE.R RMAwithCDFfilter.R simulations.R\nSODEGIR_GEstatistics.R SODEGIRpreprocessingGE.R\nSortAnnotationDataframe.R StatisticsForPREDA2dataframe.R\nStatisticsForPREDAFilterColumns_neg.R\nStatisticsForPREDAFilterColumns_pos.R\nStatisticsForPREDAFromdataframe.R statisticsForPREDAfromEset.R\nStatisticsForPREDAFromfile.R", "biocViews": "Software, CopyNumberVariation, GeneExpression, Genetics", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:35:39 UTC", "RemoteUrl": "https://github.com/bioc/PREDA", "RemoteRef": "HEAD", "RemoteSha": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:07:23 UTC", "User": "root" }, "MD5sum": "e84295ff6d834fe49c5ebf74bd05630b", "_user": "bioc", "_type": "src", "_file": "PREDA_1.59.0.tar.gz", "_fileid": "3aab81283399004a29132de4b740d510f1e5e132e3da65b94bf1422dc56c9f4d", "_filesize": 2083997, "_sha256": "3aab81283399004a29132de4b740d510f1e5e132e3da65b94bf1422dc56c9f4d", "_created": "2026-05-30T07:07:23.000Z", "_published": "2026-05-30T09:45:55.307Z", "_jobs": [ { "job": 78632406327, "time": 187, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306349224" }, { "job": 78632406342, "time": 239, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306355278" }, { "job": 78632406367, "time": 236, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306354835" }, { "job": 78632406316, "time": 193, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307213437" }, { "job": 78632406318, "time": 154, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307209281" }, { "job": 78632147098, "time": 278, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306327017" }, { "job": 78632406345, "time": 147, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306344429" }, { "job": 78632406329, "time": 208, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306351680" }, { "job": 78632406333, "time": 187, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306349137" }, { "job": 78632406334, "time": 175, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306347691" } ], "_bioccheck": { "error": 3, "warning": 5, "note": 20 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PREDA", "_commit": { "id": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379739 }, "_maintainer": { "name": "Francesco Ferrari", "email": "francesco.ferrari@ifom.eu", "login": "fferrari", "description": "", "uuid": 5503961 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.9.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "lokern", "version": ">= 1.0.9", "role": "Depends" }, { "package": "multtest", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "annotate", "role": "Depends" }, { "package": "quantsmooth", "role": "Suggests" }, { "package": "qvalue", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "caTools", "role": "Suggests" }, { "package": "affy", "role": "Suggests" }, { "package": "PREDAsampledata", "role": "Suggests" }, { "package": "Rmpi", "role": "Enhances" }, { "package": "rsprng", "role": "Enhances" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.59.0", "bioc": "3.24" }, { "branch": "release", "version": "1.58.0", "bioc": "3.23" } ], "_topics": [ "software", "copynumbervariation", "geneexpression", "genetics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 452, "source": "https://www.bioconductor.org/packages/stats/bioc/PREDA" }, "_mentions": 5, "_searchresults": 10, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PREDA.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "analysesNames", "computeDatasetSignature", "DataForPREDA2dataframe", "DataForPREDA2GenomicAnnotationsForPREDA", "DataForPREDA2StatisticsForPREDA", "DataForPREDAMedianCenter", "eset2GenomicAnnotations", "genomePlot", "GenomicAnnotations2dataframe", "GenomicAnnotations2GenomicAnnotationsForPREDA", "GenomicAnnotations2reference_positions", "GenomicAnnotationsExtract", "GenomicAnnotationsFilter_neg", "GenomicAnnotationsFilter_pos", "GenomicAnnotationsForPREDA2dataframe", "GenomicAnnotationsForPREDA2GenomicAnnotations", "GenomicAnnotationsForPREDA2PREDAResults", "GenomicAnnotationsForPREDAFromfile", "GenomicAnnotationsFromdataframe", "GenomicAnnotationsFromfile", "GenomicAnnotationsFromLibrary", "GenomicAnnotationsSortAndCleanNA", "GenomicRegions2dataframe", "GenomicRegionsAnnotate", "GenomicRegionsChrNumber", "GenomicRegionsComparison", "GenomicRegionsCreateRegionsIds", "GenomicRegionsFilter_neg", "GenomicRegionsFilter_pos", "GenomicRegionsFindOverlap", "GenomicRegionsFromdataframe", "GenomicRegionsFromfile", "GenomicRegionsNumber", "GenomicRegionsSpan", "GenomicRegionsTotalSpan", "getStatisticByName", "MergeStatisticAnnotations2DataForPREDA", "PREDA_main", "PREDADataAndResults2dataframe", "PREDAResults2dataframe", "PREDAResults2GenomicRegions", "PREDAResults2GenomicRegionsSingle", "PREDAResults2PREDADataAndResults", "PREDAResultsGetObservedFlags", "preprocessingGE", "SODEGIR_GEstatistics", "SODEGIRpreprocessingGE", "StatisticsForPREDA2dataframe", "StatisticsForPREDAFilterColumns_neg", "StatisticsForPREDAFilterColumns_pos", "StatisticsForPREDAFromdataframe", "statisticsForPREDAfromEset", "StatisticsForPREDAFromfile" ], "_help": [ { "page": "analysesNames", "title": "Get the names of the analyses in the from PREDA objects", "topics": [ "analysesNames", "analysesNames,PREDAResults-method", "analysesNames,StatisticsForPREDA-method" ] }, { "page": "computeDatasetSignature", "title": "Function to compute dataset signature for recurrent significant genomic regions", "topics": [ "computeDatasetSignature", "computeDatasetSignature,GenomicAnnotationsForPREDA-method" ] }, { "page": "DataForPREDA-class", "title": "Class \"DataForPREDA\" is used to manage all of the data required as input for PREDA analysis", "topics": [ "DataForPREDA-class" ] }, { "page": "DataForPREDA2dataframe", "title": "extract data and annotations as a dataframe", "topics": [ "DataForPREDA2dataframe", "DataForPREDA2dataframe,DataForPREDA-method" ] }, { "page": "DataForPREDA2GenomicAnnotationsForPREDA", "title": "extract a GenomicAnnotationsForPREDA object from a data DataForPREDA object", "topics": [ "DataForPREDA2GenomicAnnotationsForPREDA", "DataForPREDA2GenomicAnnotationsForPREDA,DataForPREDA-method" ] }, { "page": "DataForPREDA2StatisticsForPREDA", "title": "extract a StatisticsForPREDA object from a data DataForPREDA object", "topics": [ "DataForPREDA2StatisticsForPREDA", "DataForPREDA2StatisticsForPREDA,DataForPREDA-method" ] }, { "page": "DataForPREDAMedianCenter", "title": "Function to scale median value of DataForPREDA statistics to zero", "topics": [ "DataForPREDAMedianCenter", "DataForPREDAMedianCenter,DataForPREDA-method" ] }, { "page": "eset2GenomicAnnotations", "title": "Function building a GenomicAnnotations object on an ExpressionSet object", "topics": [ "eset2GenomicAnnotations", "eset2GenomicAnnotations,ExpressionSet-method" ] }, { "page": "genomePlot", "title": "draw a genome plot", "topics": [ "genomePlot", "genomePlot,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotations-class", "title": "Class \"GenomicAnnotations\" to manage information about genomic features", "topics": [ "GenomicAnnotations-class" ] }, { "page": "GenomicAnnotations2dataframe", "title": "extracts annotations as a dataframe", "topics": [ "GenomicAnnotations2dataframe", "GenomicAnnotations2dataframe,GenomicAnnotations-method", "GenomicAnnotations2dataframe,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotations2GenomicAnnotationsForPREDA", "title": "generate a GenomicAnnotationsForPREDA object from a GenomicAnnotations object", "topics": [ "GenomicAnnotations2GenomicAnnotationsForPREDA", "GenomicAnnotations2GenomicAnnotationsForPREDA,GenomicAnnotations-method" ] }, { "page": "GenomicAnnotations2reference_positions", "title": "extract reference positions from the GenomicAnnotations", "topics": [ "GenomicAnnotations2reference_positions", "GenomicAnnotations2reference_positions,GenomicAnnotations-method" ] }, { "page": "GenomicAnnotationsExtract", "title": "extract optional annotations for a specific region", "topics": [ "GenomicAnnotationsExtract", "GenomicAnnotationsExtract,GenomicAnnotations-method" ] }, { "page": "GenomicAnnotationsFilter_neg", "title": "filter annotations to remove selected chromosomes", "topics": [ "GenomicAnnotationsFilter_neg", "GenomicAnnotationsFilter_neg,DataForPREDA-method", "GenomicAnnotationsFilter_neg,GenomicAnnotations-method", "GenomicAnnotationsFilter_neg,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotationsFilter_pos", "title": "filter annotations to keep selected chromosomes", "topics": [ "GenomicAnnotationsFilter_pos", "GenomicAnnotationsFilter_pos,DataForPREDA-method", "GenomicAnnotationsFilter_pos,GenomicAnnotations-method", "GenomicAnnotationsFilter_pos,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotationsForPREDA-class", "title": "Class \"GenomicAnnotationsForPREDA\" GenomicAnnotations class with additional slot specifying the reference position for PREDA analysis", "topics": [ "GenomicAnnotationsForPREDA-class" ] }, { "page": "GenomicAnnotationsForPREDA2dataframe", "title": "extract annotations as a dataframe", "topics": [ "GenomicAnnotationsForPREDA2dataframe", "GenomicAnnotationsForPREDA2dataframe,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotationsForPREDA2GenomicAnnotations", "title": "extract the GenomicAnnotations object from the GenomicAnnotationsForPREDA object", "topics": [ "GenomicAnnotationsForPREDA2GenomicAnnotations", "GenomicAnnotationsForPREDA2GenomicAnnotations,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotationsForPREDA2PREDAResults", "title": "add PREDA results information to genomic annotatations creating a PREDAResults object", "topics": [ "GenomicAnnotationsForPREDA2PREDAResults", "GenomicAnnotationsForPREDA2PREDAResults,GenomicAnnotationsForPREDA-method" ] }, { "page": "GenomicAnnotationsForPREDAFromfile", "title": "Function to create a GenomicAnnotationsForPREDA object from a txt file", "topics": [ "GenomicAnnotationsForPREDAFromfile" ] }, { "page": "GenomicAnnotationsFromdataframe", "title": "Function to create a GenomiAnnotations object from a dataframe", "topics": [ "GenomicAnnotationsFromdataframe" ] }, { "page": "GenomicAnnotationsFromfile", "title": "Function to create a GenomiAnnotations object from a text file", "topics": [ "GenomicAnnotationsFromfile" ] }, { "page": "GenomicAnnotationsFromLibrary", "title": "Function extracting a GenomicAnnotations object from a Bioconductor annotation library", "topics": [ "GenomicAnnotationsFromLibrary" ] }, { "page": "GenomicAnnotationsSortAndCleanNA", "title": "sort annotations according to selected chromosomes and to remove genes containing any NA annotation field", "topics": [ "GenomicAnnotationsSortAndCleanNA", "GenomicAnnotationsSortAndCleanNA,DataForPREDA-method", "GenomicAnnotationsSortAndCleanNA,GenomicAnnotations-method", "GenomicAnnotationsSortAndCleanNA,GenomicAnnotationsForPREDA-method", "GenomicAnnotationsSortAndCleanNA,PREDADataAndResults-method", "GenomicAnnotationsSortAndCleanNA,PREDAResults-method" ] }, { "page": "GenomicRegions-class", "title": "Class \"GenomicRegions\" is used to manage information about genomic regions", "topics": [ "GenomicRegions-class" ] }, { "page": "GenomicRegions2dataframe", "title": "extract genomic regions information as a dataframe object", "topics": [ "GenomicRegions2dataframe" ] }, { "page": "GenomicRegionsAnnotate", "title": "extract annotations from a GenomicAnnotations object for a set of regions specified as a GenomicRegions object", "topics": [ "GenomicRegionsAnnotate", "GenomicRegionsAnnotate,GenomicRegions,GenomicAnnotations-method" ] }, { "page": "GenomicRegionsChrNumber", "title": "determine the number of chromosomes with genomic regions", "topics": [ "GenomicRegionsChrNumber", "GenomicRegionsChrNumber,GenomicRegions-method" ] }, { "page": "GenomicRegionsComparison", "title": "compare GenomicRegions objects to identify overlaps and differences", "topics": [ "GenomicRegionsComparison", "GenomicRegionsComparison,GenomicRegions,GenomicRegions-method" ] }, { "page": "GenomicRegionsCreateRegionsIds", "title": "generate unique ids for GenomicRegions objects", "topics": [ "GenomicRegionsCreateRegionsIds", "GenomicRegionsCreateRegionsIds,GenomicRegions-method" ] }, { "page": "GenomicRegionsFilter_neg", "title": "filter genomic regions to remove selected chromosomes", "topics": [ "GenomicRegionsFilter_neg", "GenomicRegionsFilter_neg,GenomicRegions-method" ] }, { "page": "GenomicRegionsFilter_pos", "title": "filter genomic regions to keep selected chromosomes", "topics": [ "GenomicRegionsFilter_pos", "GenomicRegionsFilter_pos,GenomicRegions-method" ] }, { "page": "GenomicRegionsFindOverlap", "title": "Function to find overlap between GenomicRegions objects", "topics": [ "GenomicRegionsFindOverlap" ] }, { "page": "GenomicRegionsFromdataframe", "title": "Function to create a GenomiRegions object from a dataframe", "topics": [ "GenomicRegionsFromdataframe" ] }, { "page": "GenomicRegionsFromfile", "title": "Function to create a GenomiRegions object from a text file", "topics": [ "GenomicRegionsFromfile" ] }, { "page": "GenomicRegionsNumber", "title": "determine the number of genomic regions", "topics": [ "GenomicRegionsNumber", "GenomicRegionsNumber,GenomicRegions-method" ] }, { "page": "GenomicRegionsSpan", "title": "determine the span of each genomic region", "topics": [ "GenomicRegionsSpan", "GenomicRegionsSpan,GenomicRegions-method" ] }, { "page": "GenomicRegionsTotalSpan", "title": "determine the total span of genomic regions", "topics": [ "GenomicRegionsTotalSpan", "GenomicRegionsTotalSpan,GenomicRegions-method" ] }, { "page": "getStatisticByName", "title": "extract data for individual analyses using the analysis name", "topics": [ "getStatisticByName", "getStatisticByName,StatisticsForPREDA-method" ] }, { "page": "MergeStatisticAnnotations2DataForPREDA", "title": "Merge a StatisticsForPREDA and a GenomicAnnotationsForPREDA object into a DataForPREDA object.", "topics": [ "MergeStatisticAnnotations2DataForPREDA" ] }, { "page": "PREDA_main", "title": "function performing the core of PREDA analysis", "topics": [ "PREDA_main" ] }, { "page": "PREDADataAndResults-class", "title": "Class \"PREDADataAndResults\" is used to manage the PREDA analysis output", "topics": [ "PREDADataAndResults-class" ] }, { "page": "PREDADataAndResults2dataframe", "title": "extract data and annotations as a dataframe with probeids as rownames", "topics": [ "PREDADataAndResults2dataframe", "PREDADataAndResults2dataframe,PREDADataAndResults-method" ] }, { "page": "PREDAResults-class", "title": "Class \"PREDAResults\" ~is used to manage the PREDA analysis output", "topics": [ "PREDAResults-class" ] }, { "page": "PREDAResults2dataframe", "title": "extact preda results statistics as a data frame object", "topics": [ "PREDAResults2dataframe", "PREDAResults2dataframe,PREDAResults-method" ] }, { "page": "PREDAResults2GenomicRegions", "title": "identify significant genomic regions from a PREDAResults object", "topics": [ "PREDAResults2GenomicRegions", "PREDAResults2GenomicRegions,PREDAResults-method" ] }, { "page": "PREDAResults2GenomicRegionsSingle", "title": "identify significant genomic regions from a single analysis in a PREDAResults object", "topics": [ "PREDAResults2GenomicRegionsSingle", "PREDAResults2GenomicRegionsSingle,PREDAResults-method" ] }, { "page": "PREDAResults2PREDADataAndResults", "title": "merge PREDAResults and input statistics to create a PREDADataAndResults object", "topics": [ "PREDAResults2PREDADataAndResults", "PREDAResults2PREDADataAndResults,PREDAResults-method" ] }, { "page": "PREDAResultsGetObservedFlags", "title": "extract genomic positions with significant alterations as a matrix of flags from a PREDAResults object", "topics": [ "PREDAResultsGetObservedFlags", "PREDAResultsGetObservedFlags,PREDAResults-method" ] }, { "page": "preprocessingGE", "title": "Wrapper function for gene expression data preprocessing for differential expression analysis with PREDA", "topics": [ "preprocessingGE" ] }, { "page": "SODEGIR_GEstatistics", "title": "Wrapper function for gene expression statistics preprocessing for SODEGIR analysis", "topics": [ "SODEGIR_GEstatistics", "SODEGIR_GEstatistics,ExpressionSet-method" ] }, { "page": "SODEGIRpreprocessingGE", "title": "Wrapper function for gene expression data preprocessing for SODEGIR analysis", "topics": [ "SODEGIRpreprocessingGE" ] }, { "page": "StatisticsForPREDA-class", "title": "Class \"StatisticsForPREDA\" is used to manage the datamatrix containing statistics for PREDA analyses", "topics": [ "StatisticsForPREDA-class" ] }, { "page": "StatisticsForPREDA2dataframe", "title": "extract data as a dataframe with probeids as rownames", "topics": [ "StatisticsForPREDA2dataframe", "StatisticsForPREDA2dataframe,StatisticsForPREDA-method" ] }, { "page": "StatisticsForPREDAFilterColumns_neg", "title": "filter statistics to remove selected analyses", "topics": [ "StatisticsForPREDAFilterColumns_neg", "StatisticsForPREDAFilterColumns_neg,DataForPREDA-method", "StatisticsForPREDAFilterColumns_neg,StatisticsForPREDA-method" ] }, { "page": "StatisticsForPREDAFilterColumns_pos", "title": "filter statistics to keep selected analyses", "topics": [ "StatisticsForPREDAFilterColumns_pos", "StatisticsForPREDAFilterColumns_pos,DataForPREDA-method", "StatisticsForPREDAFilterColumns_pos,StatisticsForPREDA-method" ] }, { "page": "StatisticsForPREDAFromdataframe", "title": "Function to create a StatisticsForPREDA objet from a dataframe", "topics": [ "StatisticsForPREDAFromdataframe" ] }, { "page": "statisticsForPREDAfromEset", "title": "function to compute a statisticsForPREDA object from an ExpressionSet object", "topics": [ "statisticsForPREDAfromEset", "statisticsForPREDAfromEset,ExpressionSet-method" ] }, { "page": "StatisticsForPREDAFromfile", "title": "Function to create a StatisticsForPREDA objet from a txt file", "topics": [ "StatisticsForPREDAFromfile" ] } ], "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "fastmap", "generics", "glue", "httr", "IRanges", "jsonlite", "KEGGREST", "lattice", "lifecycle", "lokern", "MASS", "Matrix", "memoise", "mime", "multtest", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "sfsmisc", "survival", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "PREDAclasses.Rnw", "filename": "PREDAclasses.pdf", "title": "PREDA S4-classes", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:20:11", "modified": "2018-09-14 06:30:18", "commits": 2 }, { "source": "PREDAtutorial.Rnw", "filename": "PREDAtutorial.pdf", "title": "PREDA tutorial", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:20:11", "modified": "2018-09-14 06:30:18", "commits": 4 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "preda", "_universes": [ "bioc", "fferrari" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.59.0", "date": "2026-05-30T07:10:32.000Z", "distro": "noble", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "e523d0b2121a8021262bb2f6e706a78950523651379044b6b9a1e8fc36e03f20", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.6.0", "os": "linux", "version": "1.59.0", "date": "2026-05-30T07:10:26.000Z", "distro": "noble", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "dafb0690c696d4d841409e95442c23caba8fb22fcbaff36be6289f156b38bdb1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.5.3", "os": "mac", "version": "1.59.0", "date": "2026-05-30T09:33:29.000Z", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "c686956bbcfe0b7b17ae010c224961f358b429706939a6714dd72e4561e963f0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.6.0", "os": "mac", "version": "1.59.0", "date": "2026-05-30T09:33:01.000Z", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "4cb252daec32097fb61dccb23c06a04c0bbe53a951d1404aa2d895149610424a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.6.0", "os": "wasm", "version": "1.59.0", "date": "2026-05-30T07:10:16.000Z", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "6d2fc344bf521e3014389a713639973a68fbd56ce061a75cb22a5161d646a903", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.7.0", "os": "win", "version": "1.59.0", "date": "2026-05-30T07:09:43.000Z", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "eb5e98f948863b782d27e4b9ab35ad10fa3295ea62d43571a6e0c49efe2bca5b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.5.3", "os": "win", "version": "1.59.0", "date": "2026-05-30T07:09:32.000Z", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "1374a3330b39edff09ffe8879bde04654f103b6ab204e15332db6dc901d4fd31", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" }, { "r": "4.6.0", "os": "win", "version": "1.59.0", "date": "2026-05-30T07:09:28.000Z", "commit": "e2b68a82ee67ba5df66e47042b6629ca1daf9256", "fileid": "672323bb888035af858e0bd755afbcb4ab7d84cddba4d512df6ca973d3680f97", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677568764" } ] }