{ "_id": "6a1acafd1d7bb097a09ddb2c", "Package": "HELP", "Version": "1.71.0", "Date": "2009-09-30", "Title": "Tools for HELP data analysis", "Author": "Reid F. Thompson , John M. Greally\n, with contributions from Mark\nReimers ", "Maintainer": "Reid F. Thompson ", "Description": "The package contains a modular pipeline for analysis of\nHELP microarray data, and includes graphical and mathematical\ntools with more general applications.", "License": "GPL (>= 2)", "biocViews": "CpGIsland, DNAMethylation, Microarray, TwoChannel,\nDataImport, QualityControl, Preprocessing, Visualization", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:32:59 UTC", "RemoteUrl": "https://github.com/bioc/HELP", "RemoteRef": "HEAD", "RemoteSha": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 08:00:14 UTC", "User": "root" }, "MD5sum": "88f341d3673f47d911f4746ee7c1bfab", "_user": "bioc", "_type": "src", "_file": "HELP_1.71.0.tar.gz", "_fileid": "b127c25035aeb0c60e0e7a7f2afc53d0fcfd61c78985ac8b3f7e020d023d8e0e", "_filesize": 1106747, "_sha256": "b127c25035aeb0c60e0e7a7f2afc53d0fcfd61c78985ac8b3f7e020d023d8e0e", "_created": "2026-05-30T08:00:14.000Z", "_published": "2026-05-30T11:33:17.551Z", "_jobs": [ { "job": 78635154196, "time": 143, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306679039" }, { "job": 78635154192, "time": 165, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306681148" }, { "job": 78635154191, "time": 169, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306681548" }, { "job": 78635154205, "time": 101, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307870627" }, { "job": 78635154206, "time": 114, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307871416" }, { "job": 78635013868, "time": 158, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306664349" }, { "job": 78635154181, "time": 88, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306673858" }, { "job": 78635154198, "time": 85, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306673353" }, { "job": 78635154209, "time": 70, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306672072" }, { "job": 78635154203, "time": 70, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306672073" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/HELP", "_commit": { "id": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379579 }, "_maintainer": { "name": "Reid F. Thompson", "email": "reid.thompson@gmail.com", "login": "reidt03", "description": "", "uuid": 21960505 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.8.0", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "graphics", "role": "Depends" }, { "package": "grDevices", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "methods", "role": "Depends" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.71.0", "bioc": "3.24" }, { "branch": "release", "version": "1.70.0", "bioc": "3.23" } ], "_topics": [ "cpgisland", "dnamethylation", "microarray", "twochannel", "dataimport", "qualitycontrol", "preprocessing", "visualization" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 478, "source": "https://www.bioconductor.org/packages/stats/bioc/HELP" }, "_mentions": 17, "_searchresults": 107, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/HELP.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calcGC", "calcPrototype", "calcTm", "combineData", "createWiggle", "exprs2", "exprs2<-", "fuzzyMatches", "getFeatures", "getSamples", "plotBins", "plotChip", "plotFeature", "plotPairs", "quantileNormalize", "readDesign", "readPairs", "readSampleKey" ], "_datasets": [ { "name": "base.stacking.thermodynamics", "title": "Base-stacking thermodynamic parameters", "object": "base.stacking.thermodynamics", "file": "base.stacking.thermodynamics.RData", "class": [ "matrix", "array" ], "fields": [ "dH", "dS" ], "rows": 16, "table": true, "tojson": true } ], "_help": [ { "page": "base.stacking.thermodynamics", "title": "Base-stacking thermodynamic parameters", "topics": [ "base.stacking.thermodynamics" ] }, { "page": "calcGC", "title": "Calculate GC percent", "topics": [ "calcGC" ] }, { "page": "calcGC-methods", "title": "Calculate GC percent (methods)", "topics": [ "calcGC,character-method", "calcGC,ExpressionSet-method", "calcGC,missing-method", "calcGC,NULL-method", "calcGC-methods" ] }, { "page": "calcPrototype", "title": "Calculate prototype", "topics": [ "calcPrototype" ] }, { "page": "calcPrototype-methods", "title": "Calculate prototype (methods)", "topics": [ "calcPrototype,ExpressionSet-method", "calcPrototype,matrix-method", "calcPrototype,missing-method", "calcPrototype,vector-method", "calcPrototype-methods" ] }, { "page": "calcTm", "title": "Calculate Tm", "topics": [ "calcTm" ] }, { "page": "calcTm-methods", "title": "Calculate Tm (methods)", "topics": [ "calcTm,character-method", "calcTm,ExpressionSet-method", "calcTm,missing-method", "calcTm,NULL-method", "calcTm-methods" ] }, { "page": "combineData", "title": "Combine data", "topics": [ "combineData" ] }, { "page": "combineData-methods", "title": "Combine data (methods)", "topics": [ "combineData,ExpressionSet,missing,missing-method", "combineData,ExpressionSet,vector,missing-method", "combineData,matrix,vector,matrix-method", "combineData,matrix,vector,missing-method", "combineData,missing,missing,missing-method", "combineData,vector,missing,missing-method", "combineData,vector,missing,vector-method", "combineData,vector,vector,missing-method", "combineData,vector,vector,vector-method", "combineData-methods" ] }, { "page": "createWiggle", "title": "Create wiggle track", "topics": [ "createWiggle" ] }, { "page": "createWiggle-methods", "title": "Create wiggle track (methods)", "topics": [ "createWiggle,ExpressionSet,matrix-method", "createWiggle,ExpressionSet,missing-method", "createWiggle,matrix,matrix-method", "createWiggle,missing,missing-method", "createWiggle,vector,matrix-method", "createWiggle-methods" ] }, { "page": "exprs2", "title": "Retrieve microarray data (for signal channel 2) from ExpressionSets", "topics": [ "exprs2", "exprs2<-" ] }, { "page": "exprs2-methods", "title": "Retrieve microarray data (for signal channel 2) from ExpressionSets (methods)", "topics": [ "exprs2,ExpressionSet-method", "exprs2,missing-method", "exprs2-methods", "exprs2<-,ExpressionSet,matrix-method", "exprs2<-,ExpressionSet,missing-method" ] }, { "page": "fuzzyMatches", "title": "Fuzzy matching", "topics": [ "fuzzyMatches" ] }, { "page": "fuzzyMatches-methods", "title": "Fuzzy matching (methods)", "topics": [ "fuzzyMatches,missing,missing-method", "fuzzyMatches,NULL,vector-method", "fuzzyMatches,vector,missing-method", "fuzzyMatches,vector,NULL-method", "fuzzyMatches,vector,vector-method", "fuzzyMatches-methods" ] }, { "page": "getFeatures", "title": "Get features (methods)", "topics": [ "getFeatures" ] }, { "page": "getFeatures-methods", "title": "Get features (methods)", "topics": [ "getFeatures,AnnotatedDataFrame,missing-method", "getFeatures,AnnotatedDataFrame,NULL-method", "getFeatures,AnnotatedDataFrame,vector-method", "getFeatures,ExpressionSet,missing-method", "getFeatures,ExpressionSet,NULL-method", "getFeatures,ExpressionSet,vector-method", "getFeatures,matrix,vector-method", "getFeatures,missing,missing-method", "getFeatures,vector,missing-method", "getFeatures,vector,NULL-method", "getFeatures,vector,vector-method", "getFeatures-methods" ] }, { "page": "getSamples", "title": "Get samples", "topics": [ "getSamples" ] }, { "page": "getSamples-methods", "title": "Get samples (methods)", "topics": [ "getSamples,ExpressionSet,missing-method", "getSamples,ExpressionSet,NULL-method", "getSamples,ExpressionSet,vector-method", "getSamples,matrix,missing-method", "getSamples,matrix,NULL-method", "getSamples,matrix,vector-method", "getSamples,missing,missing-method", "getSamples,vector,missing-method", "getSamples,vector,NULL-method", "getSamples,vector,vector-method", "getSamples-methods" ] }, { "page": "plotBins", "title": "Plot bins", "topics": [ "plotBins" ] }, { "page": "plotBins-methods", "title": "Plot bins (methods)", "topics": [ "plotBins,ExpressionSet,ExpressionSet-method", "plotBins,ExpressionSet,missing-method", "plotBins,ExpressionSet,vector-method", "plotBins,matrix,missing-method", "plotBins,missing,missing-method", "plotBins,vector,ExpressionSet-method", "plotBins,vector,missing-method", "plotBins,vector,vector-method", "plotBins-methods" ] }, { "page": "plotChip", "title": "Plot chip image", "topics": [ "plotChip" ] }, { "page": "plotChip-methods", "title": "Plot chip image (methods)", "topics": [ "plotChip,ExpressionSet,ExpressionSet,missing-method", "plotChip,ExpressionSet,missing,missing-method", "plotChip,ExpressionSet,vector,missing-method", "plotChip,matrix,missing,missing-method", "plotChip,missing,missing,missing-method", "plotChip,vector,vector,ExpressionSet-method", "plotChip,vector,vector,vector-method", "plotChip-methods" ] }, { "page": "plotFeature", "title": "Plot feature versus two-color intensity", "topics": [ "plotFeature" ] }, { "page": "plotFeature-methods", "title": "Plot feature versus two-color intensity (methods)", "topics": [ "plotFeature,ExpressionSet,missing-method", "plotFeature,ExpressionSet,vector-method", "plotFeature,matrix,vector-method", "plotFeature,missing,missing-method", "plotFeature-methods" ] }, { "page": "plotPairs", "title": "Plot tree-pairs", "topics": [ "plotPairs" ] }, { "page": "plotPairs-methods", "title": "Plot tree-pairs (methods)", "topics": [ "plotPairs,ExpressionSet-method", "plotPairs,matrix-method", "plotPairs,missing-method", "plotPairs-methods" ] }, { "page": "quantileNormalize", "title": "Quantile normalization", "topics": [ "quantileNormalize" ] }, { "page": "quantileNormalize-methods", "title": "Quantile normalization (methods)", "topics": [ "quantileNormalize,ExpressionSet,ExpressionSet-method", "quantileNormalize,ExpressionSet,missing-method", "quantileNormalize,ExpressionSet,vector-method", "quantileNormalize,matrix,missing-method", "quantileNormalize,missing,missing-method", "quantileNormalize,vector,ExpressionSet-method", "quantileNormalize,vector,missing-method", "quantileNormalize,vector,vector-method", "quantileNormalize-methods" ] }, { "page": "readDesign", "title": "Read NimbleGen design files", "topics": [ "readDesign" ] }, { "page": "readDesign-methods", "title": "Read NimbleGen design files (methods)", "topics": [ "readDesign,character,character,character-method", "readDesign,character,character,ExpressionSet-method", "readDesign,missing,missing,missing-method", "readDesign,vector,missing,missing-method", "readDesign,vector,vector,missing-method", "readDesign-methods" ] }, { "page": "readPairs", "title": "Read Nimblegen .pair files", "topics": [ "readPairs" ] }, { "page": "readPairs-methods", "title": "Read Nimblegen .pair files (methods)", "topics": [ "readPairs,character,character,character-method", "readPairs,character,character,ExpressionSet-method", "readPairs,missing,missing,missing-method", "readPairs,vector,missing,missing-method", "readPairs,vector,vector,missing-method", "readPairs-methods" ] }, { "page": "readSampleKey", "title": "Read sample key", "topics": [ "readSampleKey" ] } ], "_rundeps": [ "Biobase", "BiocGenerics", "generics" ], "_vignettes": [ { "source": "HELP.Rnw", "filename": "HELP.pdf", "title": "Primer ", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:04:13", "modified": "2013-11-01 20:04:13", "commits": 1 } ], "_score": 5.330413773349191, "_indexed": true, "_nocasepkg": "help", "_universes": [ "bioc", "reidt03" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.71.0", "date": "2026-05-30T08:02:57.000Z", "distro": "noble", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "c843c987196c92bbdbf66e9928a0a80d1dca5687a7a7d0e739d301ac5105401d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.6.0", "os": "linux", "version": "1.71.0", "date": "2026-05-30T08:02:58.000Z", "distro": "noble", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "15cf71a0ce622d425fc54b407151e4310c9a0c73c223f2fe28277cd782da8d22", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.5.3", "os": "mac", "version": "1.71.0", "date": "2026-05-30T11:32:37.000Z", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "75e17f3101b513b15de094cf0143a7b80b7834ad6120f668d94bcfa2cb9a46b8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.6.0", "os": "mac", "version": "1.71.0", "date": "2026-05-30T11:32:44.000Z", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "bdc2b8c4cc9029eba8aed12a2a976749068a45b4d25337600e2f2ce89a82b4ed", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.6.0", "os": "wasm", "version": "1.71.0", "date": "2026-05-30T08:01:59.000Z", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "025b0b62cd3cdf1d4c2ea30578cd7757b1b268aa113127d68559699eaf706025", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.7.0", "os": "win", "version": "1.71.0", "date": "2026-05-30T08:01:27.000Z", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "b7afca670a4caf6e3d551db861f0edd0c373d14f2043c55c27840bdc269e2d32", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.5.3", "os": "win", "version": "1.71.0", "date": "2026-05-30T08:01:15.000Z", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "681f5aab25dcc5c4d47b7f282ead3462cf7a466fcccc9b137361e9c3f18fd85f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" }, { "r": "4.6.0", "os": "win", "version": "1.71.0", "date": "2026-05-30T08:01:16.000Z", "commit": "74ec2b221c804df97a2d518c39ae4b281c9c3dca", "fileid": "d8b2a3a5811d3eb25b6912cf1faf218c4e6af24b7e45f69a4b9af6135acb7d13", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678642615" } ] }