{ "_id": "6aabd0ab3d719c1f8406f4a0", "Package": "davidTiling", "Version": "1.53.1", "Title": "Data and analysis scripts for David, Huber et al. yeast tiling\narray paper", "Authors@R": "c(\nperson(\"Wolfgang\", \"Huber\", email = \"wolfgang.huber@embl.org\", role = c(\"aut\", \"cre\")),\nperson(\"Joern\", \"Toedling\")\n)", "Description": "This package contains the data for the paper by L. David\net al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix\ngenechips, an ExpressionSet object with the raw feature data, a\nprobe annotation data structure for the chip and the yeast\ngenome annotation (GFF file) that was used. In addition, some\ncustom-written analysis functions are provided, as well as R\nscripts in the scripts directory.", "biocViews": "ExperimentData, Genome, Saccharomyces_cerevisiae_Data,\nMicroarrayData, ReproducibleResearch", "Reference": "A high-resolution map of transcription in the yeast genome.\nDavid L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L,\nJones T, Davis RW, Steinmetz LM. Proc Natl Acad Sci U S A. 2006\nApr 4;103(14):5320-5.", "License": "LGPL", "URL": "http://www.ebi.ac.uk/huber", "BuildResaveData": "no", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://huber-group-embl.r-universe.dev", "Date/Publication": "2026-08-18 20:17:17 UTC", "RemoteUrl": "https://github.com/Huber-group-EMBL/davidTiling", "RemoteRef": "HEAD", "RemoteSha": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-17 10:39:12 UTC", "User": "root" }, "Author": "Wolfgang Huber [aut, cre]", "Maintainer": "Wolfgang Huber ", "_user": "huber-group-embl", "_type": "src", "_file": "davidTiling_1.53.1.tar.gz", "_fileid": "https://r2.ropensci.org/05453fcf4f801ae0ccf4052f1444cd6469e8d29e098b59dbab050c726dfe873c", "_filesize": 33337402, "_sha256": "05453fcf4f801ae0ccf4052f1444cd6469e8d29e098b59dbab050c726dfe873c", "_expires": "2026-12-26T11:36:07.000Z", "_created": "2026-09-17T10:39:12.000Z", "_published": "2026-09-17T11:36:11.740Z", "_jobs": [ { "job": 105170381308, "time": 274, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10493055469" }, { "job": 105170381437, "time": 232, "config": "linux-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10491694892" }, { "job": 105170381438, "time": 181, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "10495666212" }, { "job": 105170381335, "time": 187, "config": "macos-release-arm64", "r": "4.6.1", "check": "WARNING", "artifact": "10494937536" }, { "job": 105169058811, "time": 283, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10491843464" }, { "job": 105170381263, "time": 158, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10493170210" }, { "job": 105170381361, "time": 148, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "10492072895" }, { "job": 105170381277, "time": 160, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "10492082931" }, { "job": 105170381311, "time": 165, "config": "windows-release-x86_64", "r": "4.6.1", "check": "WARNING", "artifact": "10493165205" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334", "_status": "success", "_upstream": "https://github.com/Huber-group-EMBL/davidTiling", "_commit": { "id": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "author": "Hugo Gruson ", "committer": "Hugo Gruson ", "message": "Bump version\n", "time": 1787084237 }, "_maintainer": { "name": "Wolfgang Huber", "email": "wolfgang.huber@embl.org", "login": "wolfganghuber", "twitter": "@wolfgangkhuber", "description": "www.huber.embl.org", "uuid": 5198414 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Biobase", "version": ">= 2.5.5", "role": "Depends" }, { "package": "tilingArray", "role": "Depends" }, { "package": "GO.db", "role": "Depends" }, { "package": "methods", "role": "Depends" } ], "_owner": "huber-group-embl", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 }, { "week": "2026-34", "n": 8 } ], "_tags": [], "_topics": [ "experimentdata", "genome", "saccharomyces_cerevisiae_data", "microarraydata", "reproducibleresearch" ], "_stars": 0, "_contributors": [ { "user": "hpages", "count": 18, "uuid": 8810451 }, { "user": "dtenenba", "count": 17, "uuid": 2286826 }, { "user": "bisaloo", "count": 8, "uuid": 10783929 }, { "user": "lshep", "count": 8, "uuid": 18724380 }, { "user": "nturaga", "count": 5, "uuid": 2746443 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 }, { "user": "sonali-bioc", "count": 2, "uuid": 6373953 } ], "_userbio": { "uuid": 57364287, "type": "organization", "name": "EMBL Huber Group", "followers": 20, "description": "Repository for joint projects by members and ex-members of the Huber group at EMBL. Please see also individuals' pages for further repositories." }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/davidTiling" }, "_devurl": "https://github.com/huber-group-embl/davidtiling", "_searchresults": 6, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/davidTiling.html", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt" ], "_cranurl": false, "_exports": [ "getAllGO", "getAttributeField", "getDavidTilingData", "GOHyperG", "scatterWithHist", "showDens" ], "_datasets": [ { "name": "gff", "title": "Genomic features of Saccharomyces cerevisiae", "object": "gff", "file": "gff.rda", "class": [ "data.frame" ], "fields": [ "seqname", "source", "feature", "start", "end", "score", "strand", "frame", "attributes", "Name", "orf_classification", "gene", "chr" ], "rows": 21729, "table": true, "tojson": true }, { "name": "probeAnno", "title": "An environment with probe mapping information for the Scerevisiae tiling array", "object": "probeAnno", "file": "probeAnno.rda", "class": [ "environment" ], "fields": [], "table": false, "tojson": false }, { "name": "yeastFeatures", "title": "A data.frame with metadata about the features in SGD GFF files", "object": "yeastFeatures", "file": "yeastFeatures.R", "class": [ "data.frame" ], "fields": [ "isTranscribed" ], "rows": 25, "table": true, "tojson": true } ], "_help": [ { "page": "davidTiling", "title": "Dataset of class eSet with the raw 'CEL file' intensities", "topics": [ "data:davidTiling", "davidTiling" ] }, { "page": "gff", "title": "Genomic features of Saccharomyces cerevisiae", "topics": [ "data:gff", "gff" ] }, { "page": "probeAnno", "title": "An environment with probe mapping information for the Scerevisiae tiling array", "topics": [ "data:probeAnno", "probeAnno" ] }, { "page": "getGO", "title": "Get all GO categories for a list of genes.", "topics": [ "getAllGO" ] }, { "page": "getAttributeField", "title": "Extract the value of a certain field out of a character vector such as in the \"attributes\" column of a GFF table.", "topics": [ "getAttributeField" ] }, { "page": "getDavidTilingData", "title": "Create the data set davidTiling.", "topics": [ "getDavidTilingData" ] }, { "page": "GOHyperG", "title": "Hypergeometric test for GO category enrichment.", "topics": [ "GOHyperG" ] }, { "page": "scatterWithHist", "title": "Scatterplot with histograms of marginal distributions", "topics": [ "scatterWithHist" ] }, { "page": "scoreSegments", "title": "Score segments", "topics": [ "scoreSegments" ] }, { "page": "showDens", "title": "Plot function for more than one density", "topics": [ "showDens" ] }, { "page": "yeastFeatures", "title": "A data.frame with metadata about the features in SGD GFF files", "topics": [ "yeastFeatures" ] } ], "_rundeps": [ "affy", "affyio", "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocManager", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "cpp11", "crayon", "curl", "DBI", "farver", "fastmap", "genefilter", "generics", "ggplot2", "glue", "GO.db", "gtable", "httr", "IRanges", "isoband", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "limma", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pixmap", "pkgconfig", "png", "preprocessCore", "R6", "RColorBrewer", "rlang", "RSQLite", "S4Vectors", "S7", "sandwich", "scales", "Seqinfo", "statmod", "strucchange", "survival", "sys", "tilingArray", "vctrs", "viridisLite", "vsn", "withr", "XML", "xtable", "XVector", "zoo" ], "_score": 2.255272505103306, "_indexed": true, "_nocasepkg": "davidtiling", "_universes": [ "huber-group-embl", "wolfganghuber" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.53.1", "date": "2026-09-17T10:43:06.000Z", "distro": "resolute", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/79d52d45f7a239e66b7e2810c4426635ae27aed0ca3899e9676558d8522d84dd", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.6.1", "os": "linux", "version": "1.53.1", "date": "2026-09-17T10:42:33.000Z", "distro": "resolute", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/2c334ba8666409f4fb0de627fd2762809f349cf025bb48d7a6e7ecb9c3a8bd46", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.5.3", "os": "mac", "version": "1.53.1", "date": "2026-09-17T11:34:06.000Z", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/7e3eb19418f28526631e61209a100de97e1f4ecad22fa4e61dba0c371b63d951", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.6.1", "os": "mac", "version": "1.53.1", "date": "2026-09-17T11:34:16.000Z", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/98ea1e9bd3f362b8d15bfecfdb31bd74896ed5aa1a9e88519ec5b28759928635", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.6.0", "os": "wasm", "version": "1.53.1", "date": "2026-09-17T10:42:30.000Z", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/29402a73e2629f00c2d3434bcbaded58e640de7317646ca245b5cd0976921ca7", "status": "success", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.7.0", "os": "win", "version": "1.53.1", "date": "2026-09-17T10:41:01.000Z", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/ea5ce132a0c6a78efd4a2cda719a7eba7bc2ac37704e74372d4234044ded4314", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.5.3", "os": "win", "version": "1.53.1", "date": "2026-09-17T10:41:15.000Z", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/f1d48ec031efc98775c20f9aa2b9280c34c0a7b878872deba3c723da1530a48c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" }, { "r": "4.6.1", "os": "win", "version": "1.53.1", "date": "2026-09-17T10:41:13.000Z", "commit": "c2d32bbb7c099dc50f5103c2967735d09cadbbd2", "fileid": "https://r2.ropensci.org/908c813a1482100d7cf39175bc130ba20aec30bc4ab0bd802e95f7d00eb68282", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/huber-group-embl/actions/runs/35211235334" } ] }