{ "_id": "6a498e696d67900babdfb2bb", "Package": "mCSEA", "Type": "Package", "Title": "Methylated CpGs Set Enrichment Analysis", "Version": "1.33.0", "Author": "Jordi Martorell-Marugán and Pedro Carmona-Sáez", "Maintainer": "Jordi Martorell-Marugán ", "Description": "Identification of diferentially methylated regions (DMRs)\nin predefined regions (promoters, CpG islands...) from the\nhuman genome using Illumina's 450K or EPIC microarray data.\nProvides methods to rank CpG probes based on linear models and\nincludes plotting functions.", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, DifferentialMethylation, DNAMethylation,\nEpigenetics, Genetics, GenomeAnnotation, MethylationArray,\nMicroarray, MultipleComparison, TwoChannel", "License": "GPL-2", "Encoding": "UTF-8", "LazyData": "true", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev libjpeg-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nxz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:08 UTC", "RemoteUrl": "https://github.com/bioc/mCSEA", "RemoteRef": "HEAD", "RemoteSha": "283bcc89f1f6202e967bd5449c642beae96947e2", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 22:36:31 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "mCSEA_1.33.0.tar.gz", "_fileid": "https://r2.ropensci.org/f362de5284d694e737f8d758b00342c582fab1a2fb64b94601a5bd16a9711e71", "_filesize": 1724852, "_sha256": "f362de5284d694e737f8d758b00342c582fab1a2fb64b94601a5bd16a9711e71", "_expires": "2026-10-12T22:51:19.000Z", "_created": "2026-07-04T22:36:31.000Z", "_published": "2026-07-04T22:51:21.372Z", "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392", "_status": "failure", "_upstream": "https://github.com/bioc/mCSEA", "_commit": { "id": "283bcc89f1f6202e967bd5449c642beae96947e2", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380428 }, "_maintainer": { "name": "Jordi Martorell-Marugán", "email": "jmartorellm@gmail.com", "login": "jordimartorell", "description": "", "uuid": 33520613 }, "_distro": "resolute", "_jobs": [ { "job": 85172729253, "time": 591, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8086110843" }, { "job": 85172729239, "time": 734, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "8086126297" }, { "job": 85172729243, "time": 822, "config": "linux-release-x86_64", "r": "4.6.1", "check": "ERROR", "artifact": "8086136221" }, { "job": 85172729246, "time": 453, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "8086095969" }, { "job": 85172729248, "time": 519, "config": "macos-release-arm64", "r": "4.6.1", "check": "ERROR", "artifact": "8086102966" }, { "job": 85172015191, "time": 710, "config": "source", "r": "4.6.1", "check": "ERROR", "artifact": "8086045556" }, { "job": 85172729249, "time": 538, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8086105135" }, { "job": 85172729245, "time": 586, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "8086110430" }, { "job": 85172729242, "time": 682, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "8086120936" }, { "job": 85172729244, "time": 693, "config": "windows-release", "r": "4.6.1", "check": "ERROR", "artifact": "8086121832" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "mCSEAdata", "role": "Depends" }, { "package": "Homo.sapiens", "role": "Depends" }, { "package": "biomaRt", "role": "Imports" }, { "package": "fgsea", "role": "Imports" }, { "package": "GenomicFeatures", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "Gviz", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Biobase", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "FlowSorted.Blood.450k", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "leukemiasEset", "role": "Suggests" }, { "package": "minfi", "role": "Suggests" }, { "package": "minfiData", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2025-46", "n": 1 }, { "week": "2025-47", "n": 1 }, { "week": "2025-48", "n": 1 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "differentialmethylation", "dnamethylation", "epigenetics", "genetics", "genomeannotation", "methylationarray", "microarray", "multiplecomparison", "twochannel" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 4, "_searchresults": 21, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/mCSEA.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "mCSEAIntegrate", "mCSEAPlot", "mCSEAPlotGSEA", "mCSEATest", "rankProbes" ], "_datasets": [ { "name": "exprTest", "title": "Expression data example", "object": "exprTest", "class": [ "matrix", "array" ], "fields": [ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20" ], "rows": 101, "table": true, "tojson": true }, { "name": "myRank", "title": "Precomputed mCSEA results", "object": "precomputedmCSEA", "class": [ "numeric" ], "fields": [], "table": false, "tojson": true }, { "name": "myResults", "title": "Precomputed mCSEA results", "object": "precomputedmCSEA", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "mCSEA-package", "title": "Methylated CpGs Set Enrichment Analysis", "topics": [ "mCSEA-package", "mCSEA" ] }, { "page": "exprTest", "title": "Expression data example", "topics": [ "exprTest" ] }, { "page": "mCSEAIntegrate", "title": "Integrate methylation and expression", "topics": [ "mCSEAIntegrate" ] }, { "page": "mCSEAPlot", "title": "Plot mCSEA results", "topics": [ "mCSEAPlot" ] }, { "page": "mCSEAPlotGSEA", "title": "Plot mCSEA results", "topics": [ "mCSEAPlotGSEA" ] }, { "page": "mCSEATest", "title": "mCSEA core analysis", "topics": [ "mCSEATest" ] }, { "page": "precomputedmCSEA", "title": "Precomputed mCSEA results", "topics": [ "myRank", "myResults", "precomputedmCSEA" ] }, { "page": "rankProbes", "title": "Rank CpG probes", "topics": [ "rankProbes" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "backports", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "biomaRt", "Biostrings", "biovizBase", "bit", "bit64", "bitops", "blob", "BSgenome", "bslib", "cachem", "checkmate", "cigarillo", "cli", "cluster", "codetools", "colorspace", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "deldir", "dichromat", "digest", "dplyr", "ensembldb", "evaluate", "farver", "fastmap", "fastmatch", "fgsea", "filelock", "fontawesome", "foreign", "formatR", "Formula", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggplot2", "glue", "GO.db", "graph", "gridExtra", "gtable", "Gviz", "highr", "Hmisc", "hms", "Homo.sapiens", "htmlTable", "htmltools", "htmlwidgets", "httr", "httr2", "interp", "IRanges", "isoband", "jpeg", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "lambda.r", "lattice", "latticeExtra", "lazyeval", "lifecycle", "limma", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mCSEAdata", "memoise", "mime", "nnet", "openssl", "org.Hs.eg.db", "OrganismDbi", "pillar", "pkgconfig", "png", "prettyunits", "progress", "ProtGenerics", "purrr", "R6", "rappdirs", "RBGL", "RColorBrewer", "Rcpp", "RcppEigen", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "rmarkdown", "rpart", "Rsamtools", "RSQLite", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "TxDb.Hsapiens.UCSC.hg19.knownGene", "UCSC.utils", "utf8", "VariantAnnotation", "vctrs", "viridisLite", "withr", "xfun", "XML", "xml2", "XVector", "yaml" ], "_score": 3.623249290397901, "_indexed": true, "_nocasepkg": "mcsea", "_universes": [ "bioc", "jordimartorell" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.33.0", "date": "2026-07-04T22:45:33.000Z", "distro": "resolute", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/a410adb7d9c7e2914b5b17a8079a325f88ec6530260bb56c081b06d669e24a4e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.6.1", "os": "linux", "version": "1.33.0", "date": "2026-07-04T22:46:26.000Z", "distro": "resolute", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/a9a83f73d5c875d6963543750686e1d07f58abc96f822c0516e6c3b4ed21728b", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.5.3", "os": "mac", "version": "1.33.0", "date": "2026-07-04T22:41:22.000Z", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/5e77b33f6d9aec60cb5bb761a77d89230296c38fae149981323615266672b596", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.6.1", "os": "mac", "version": "1.33.0", "date": "2026-07-04T22:42:42.000Z", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/815b0cccbfe7262a13c191ff27cbe3d56754351d0c783610f133f1216ae636da", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.6.0", "os": "wasm", "version": "1.33.0", "date": "2026-07-04T22:46:06.000Z", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/0575c591cab39b7e271e4a4da332a6f0a4688e0a48ee935e157d821d79c1215b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.7.0", "os": "win", "version": "1.33.0", "date": "2026-07-04T22:43:27.000Z", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/780066894a0aeb0288dda45d66eb7f4cdd716116ede7d917acc9d8fb8278c8d8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.5.3", "os": "win", "version": "1.33.0", "date": "2026-07-04T22:44:05.000Z", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/ac1f4258af1bdc0120b41f19ecd79c9a73acdab0f0e1e704a50901dea6149ab8", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" }, { "r": "4.6.1", "os": "win", "version": "1.33.0", "date": "2026-07-04T22:44:14.000Z", "commit": "283bcc89f1f6202e967bd5449c642beae96947e2", "fileid": "https://r2.ropensci.org/3434bd7192f69652dedd25fd1dd85a393ba33697b0b5dec1660835a5e2596725", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28721590392" } ] }