{ "_id": "6a13f07cacfb0bcc41d304de", "Package": "cn.farms", "Title": "cn.FARMS - factor analysis for copy number estimation", "Version": "1.60.0", "Date": "2025-07-12", "Type": "Package", "License": "LGPL (>= 2.0)", "Author": "Andreas Mitterecker, Djork-Arne Clevert", "Maintainer": "Andreas Mitterecker ", "Description": "This package implements the cn.FARMS algorithm for copy\nnumber variation (CNV) analysis. cn.FARMS allows to analyze the\nmost common Affymetrix (250K-SNP6.0) array types, supports\nhigh-performance computing using snow and ff.", "URL": "http://www.bioinf.jku.at/software/cnfarms/cnfarms.html", "Collate": "'callSummarize.R' 'combineData.R' 'correctPkgname.R'\n'cnFarms.R' 'createAnnotation.R' 'createMatrix.R'\n'determineBaselineArray.R' 'distributionDistance.R'\n'dnaCopySf.R' 'doCnFarms.R' 'fragLengthCorr.R' 'normAdd.R'\n'normalizeAverage.R' 'normalizeCels.R' 'normalizeNpData.R'\n'normalizeQuantiles.R' 'normalizeSor.R' 'plotDendrogram.R'\n'plotDensity.R' 'plotEvalIc.R' 'plotSmoothScatter.R'\n'plotsRegions.R' 'plotViolines.R' 'sparseFarmsC.R'\n'summarizationMl.R' 'summarizationSl.R'\n'summarizeFarmsGaussian.R' 'summarizeFarmsLaplaceExact.R'\n'summarizeFarmsLaplaceVar.R' 'summarizeFarmsMethods.R'\n'summarizeStatistics.R' 'windowFunctions.R' 'windowMethods.R'\n'normalizeProbeSequence.R' 'snowfallExt.R'\n'summarizeFarmsLaplaceExact2.R' 'summarizeFarmsLaplaceExact3.R'\n'normalizeNone.R' 'utils-lds.R' 'zzz.R' 'sFclusterFunctions.R'\n'sFinit.R' 'sFsnowfall-internal.R' 'sFsnowWrappers.R'\n'sFsocketRequest.R' 'vanillaIce.R'", "biocViews": "Microarray, CopyNumberVariation", "Roxygen": "list(wrap = FALSE)", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:35:15 UTC", "RemoteUrl": "https://github.com/bioc/cn.farms", "RemoteRef": "RELEASE_3_23", "RemoteSha": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-25 06:38:18 UTC", "User": "root" }, "MD5sum": "f66c69d652ec78811be8cb72ca97ea5e", "_user": "bioc-release", "_type": "src", "_file": "cn.farms_1.60.0.tar.gz", "_fileid": "2a1a9da06097c7cd7cdd0178996713c6db4cbb427f62f126bc127087866f7458", "_filesize": 2515678, "_sha256": "2a1a9da06097c7cd7cdd0178996713c6db4cbb427f62f126bc127087866f7458", "_created": "2026-05-25T06:38:18.000Z", "_published": "2026-05-25T06:47:23.999Z", "_jobs": [ { "job": 77668060235, "time": 159, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7193031659" }, { "job": 77668060325, "time": 255, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7193053198" }, { "job": 77668060320, "time": 312, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7193066196" }, { "job": 77668060335, "time": 244, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7193050580" }, { "job": 77668060317, "time": 308, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7193064741" }, { "job": 77668060268, "time": 164, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7193032627" }, { "job": 77668060261, "time": 339, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7193072520" }, { "job": 77668060263, "time": 197, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7193040058" }, { "job": 77668060266, "time": 484, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7193104003" }, { "job": 77667610089, "time": 245, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7192992152" }, { "job": 77668060233, "time": 107, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7193018908" }, { "job": 77668060298, "time": 296, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7193061832" }, { "job": 77668060311, "time": 244, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7193050978" }, { "job": 77668060308, "time": 239, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7193049730" } ], "_bioccheck": { "error": 2, "warning": 5, "note": 19 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/cn.farms", "_commit": { "id": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777379715 }, "_maintainer": { "name": "Andreas Mitterecker", "email": "mitteran11@gmail.com" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "ff", "role": "Depends" }, { "package": "oligoClasses", "role": "Depends" }, { "package": "snow", "role": "Depends" }, { "package": "DBI", "role": "Imports" }, { "package": "affxparser", "role": "Imports" }, { "package": "oligo", "role": "Imports" }, { "package": "DNAcopy", "role": "Imports" }, { "package": "preprocessCore", "role": "Imports" }, { "package": "lattice", "role": "Imports" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-28", "n": 2 }, { "week": "2025-29", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.61.0", "bioc": "3.24" }, { "branch": "release", "version": "1.60.0", "bioc": "3.23" } ], "_topics": [ "microarray", "copynumbervariation", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 435, "source": "https://www.bioconductor.org/packages/stats/bioc/cn.farms" }, "_searchresults": 7, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/cn.farms.html", "extra/contents.json", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "cn.farms", "cnLibrary", "combineData", "createAnnotation", "createMatrix", "distributionDistance", "dnaCopySf", "fragLengCorr", "mlSummarization", "normalizeAverage", "normalizeCels", "normalizeNpData", "normalizeSequenceEffect", "plotDendrogram", "plotDensity", "plotEvalIc", "plotRegions", "plotSmoothScatter", "plotViolines", "slSummarization", "sparseFarmsC", "summarizeFarmsExact", "summarizeFarmsExact2", "summarizeFarmsExact3", "summarizeFarmsGaussian", "summarizeFarmsMethods", "summarizeFarmsStatistics", "summarizeFarmsVariational", "summarizeWindowBps", "summarizeWindowMethods", "summarizeWindowStd" ], "_help": [ { "page": "callSummarize", "title": "Defines which variables should be written back when calling a cn.farms run", "topics": [ "callSummarize" ] }, { "page": "cn.farms", "title": "cn.farms", "topics": [ "cn.farms" ] }, { "page": "cnLibrary", "title": "This function was taken from snowfall and edited due to some deprecated function calls.", "topics": [ "cnLibrary" ] }, { "page": "combineData", "title": "Combine two ExpressionSet objects", "topics": [ "combineData" ] }, { "page": "createAnnotation", "title": "Creation of annotation files", "topics": [ "createAnnotation" ] }, { "page": "createMatrix", "title": "Creates the needed matrix", "topics": [ "createMatrix" ] }, { "page": "distributionDistance", "title": "Computes the distribution distance", "topics": [ "distributionDistance" ] }, { "page": "dnaCopySf", "title": "Runs DNAcopy in parallel mode", "topics": [ "dnaCopySf" ] }, { "page": "doCnFarmsSingle", "title": "Does the whole cn.farms process in one call", "topics": [ "doCnFarmsSingle" ] }, { "page": "flcSnp6Std", "title": "Does a fragment length correction on intensities", "topics": [ "flcSnp6Std" ] }, { "page": "flcStd", "title": "Does a fragment length correction on intensities", "topics": [ "flcStd" ] }, { "page": "fragLengCorr", "title": "Does a fragment length correction", "topics": [ "fragLengCorr" ] }, { "page": "getFragmentSet", "title": "Finds SNPs which belong to one fragment", "topics": [ "getFragmentSet" ] }, { "page": "getSingleProbeSetSize", "title": "Combines data for probeset summarization", "topics": [ "getSingleProbeSetSize" ] }, { "page": "mlSummarization", "title": "Method for computation of the multi-loci summarization", "topics": [ "mlSummarization" ] }, { "page": "normAdd", "title": "Extracts info from the package name", "topics": [ "normAdd" ] }, { "page": "normalizeAverage", "title": "Scales the range of the non-polymorphic data to the range of a given array.", "topics": [ "normalizeAverage" ] }, { "page": "normalizeCels", "title": "Wrapper for the normalization functions", "topics": [ "normalizeCels" ] }, { "page": "normalizeNone", "title": "Runs the SOR normalization on microarray data", "topics": [ "normalizeNone" ] }, { "page": "normalizeNpData", "title": "Processes the non-polymorphic data", "topics": [ "normalizeNpData" ] }, { "page": "normalizeQuantiles", "title": "Normalization Quantiles", "topics": [ "normalizeQuantiles" ] }, { "page": "normalizeSequenceEffect", "title": "Correction for probe sequence effects", "topics": [ "normalizeSequenceEffect" ] }, { "page": "normalizeSor", "title": "Runs the SOR normalization on microarray data", "topics": [ "normalizeSor" ] }, { "page": "plotDendrogram", "title": "Plots a dendrogram", "topics": [ "plotDendrogram" ] }, { "page": "plotDensity", "title": "Function to create a density plot", "topics": [ "plotDensity" ] }, { "page": "plotEvalIc", "title": "Creates a plot with known regions and a numeric vector", "topics": [ "plotEvalIc" ] }, { "page": "plotRegions", "title": "Plots given regions by segments", "topics": [ "plotRegions" ] }, { "page": "plotSmoothScatter", "title": "Creates a smooth scatter plot", "topics": [ "plotSmoothScatter" ] }, { "page": "plotViolines", "title": "Create a violine plot", "topics": [ "plotViolines" ] }, { "page": "slSummarization", "title": "Method for computation of the single-locus summarization", "topics": [ "slSummarization" ] }, { "page": "sparseFarmsC", "title": "Normalizes the data with SOR", "topics": [ "sparseFarmsC" ] }, { "page": "summarizeFarmsExact", "title": "Summarization Laplacian approach with exact computation", "topics": [ "summarizeFarmsExact" ] }, { "page": "summarizeFarmsExact2", "title": "Summarization Laplacian approach with exact computation", "topics": [ "summarizeFarmsExact2" ] }, { "page": "summarizeFarmsExact3", "title": "Summarization Laplacian approach with exact computation", "topics": [ "summarizeFarmsExact3" ] }, { "page": "summarizeFarmsGaussian", "title": "Summarization Gaussian approach", "topics": [ "summarizeFarmsGaussian" ] }, { "page": "summarizeFarmsMethods", "title": "Lists methods for possible FARMS summarization", "topics": [ "summarizeFarmsMethods" ] }, { "page": "summarizeFarmsStatistics", "title": "Mean or median instead of the FARMS model", "topics": [ "summarizeFarmsStatistics" ] }, { "page": "summarizeFarmsVariational", "title": "Summarization variational Laplacian approach", "topics": [ "summarizeFarmsVariational" ] }, { "page": "summarizeWindowBps", "title": "Combines neighbouring locations to windows", "topics": [ "summarizeWindowBps" ] }, { "page": "summarizeWindowMethods", "title": "Lists methods for possible window methods", "topics": [ "summarizeWindowMethods" ] }, { "page": "summarizeWindowStd", "title": "Combines neighbouring locations to windows", "topics": [ "summarizeWindowStd" ] } ], "_rundeps": [ "abind", "affxparser", "affyio", "Biobase", "BiocGenerics", "BiocManager", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "DBI", "DelayedArray", "DNAcopy", "fastmap", "ff", "foreach", "generics", "GenomicRanges", "glue", "IRanges", "iterators", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "oligo", "oligoClasses", "pkgconfig", "preprocessCore", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "vctrs", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "cn.farms.Rnw", "filename": "cn.farms.pdf", "title": "cn.farms: Manual for the R package", "engine": "utils::Sweave", "headings": [], "created": "2012-11-06 15:37:41", "modified": "2014-05-16 11:31:22", "commits": 4 } ], "_score": 3.6020599913279625, "_indexed": false, "_nocasepkg": "cn.farms", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/cn.farms", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.60.0", "date": "2026-05-25T06:40:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "4530b554656102ea4b3fff635cfdebf4f233e08f95d80f812d6fea1ede6288b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.7.0", "os": "linux", "version": "1.60.0", "date": "2026-05-25T06:41:42.000Z", "distro": "noble", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "c78166670ae70eb4ee6ec6ec4a257ee9d3f176ac5966825a0ce97a38a550fcb9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.6.0", "os": "linux", "version": "1.60.0", "date": "2026-05-25T06:40:55.000Z", "distro": "noble", "arch": "aarch64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "34f9972cb79b04d7de71ba74eef85e5bd9a8df364604e1d4e93112636a8666db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.6.0", "os": "linux", "version": "1.60.0", "date": "2026-05-25T06:41:38.000Z", "distro": "noble", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "039e3b1382ae757862e7931fdc15c663f582f814d5b9dd97ab568e32ae471b01", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.5.3", "os": "mac", "version": "1.60.0", "date": "2026-05-25T06:40:07.000Z", "arch": "aarch64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "8b90d48edb1e1ecc04845f2296b53686c72c601408ef58e20cdfe7811ac606e8", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.5.3", "os": "mac", "version": "1.60.0", "date": "2026-05-25T06:41:14.000Z", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "46f2eb9ba48804577403dfc326839e2816e1ea03f1993906bf71e5a71ec1b472", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.6.0", "os": "mac", "version": "1.60.0", "date": "2026-05-25T06:40:17.000Z", "arch": "aarch64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "fd7263dea292cc716ea60a164d7cdc431dc39fb43783471d5774588ce7fc62b6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.6.0", "os": "mac", "version": "1.60.0", "date": "2026-05-25T06:42:03.000Z", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "883c2ccbebe7af1e5f4c2182a5e408090161c05512c20b57fe6df3622c48fe08", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.6.0", "os": "wasm", "version": "1.60.0", "date": "2026-05-25T06:40:41.000Z", "arch": "emscripten", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "b864da4a019f251a28162da2db9583a9e139b34d0c623233ef6dae6916948f9f", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.7.0", "os": "win", "version": "1.60.0", "date": "2026-05-25T06:40:42.000Z", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "225011e704a6e84cc3ccea3168fab8bbbde65b5742e77db92ce355185366cc36", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.5.3", "os": "win", "version": "1.60.0", "date": "2026-05-25T06:39:57.000Z", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "2487da1c8c438be8037f4cab50d2b7ffcedd39a4ecc816a99fd3df881e70c82b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" }, { "r": "4.6.0", "os": "win", "version": "1.60.0", "date": "2026-05-25T06:39:54.000Z", "arch": "x86_64", "commit": "dd7a1f5fe94c3e66c0581e63b595b542a6875f36", "fileid": "f00629f99398859e34fdb887b20fe39e18fc21789731050abb6c1ff79c91f559", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386977065" } ] }