{ "_id": "6a494e3af6c47c441949a089", "Package": "shinyepico", "Title": "ShinyÉPICo", "Version": "1.21.0", "Authors@R": "person('Octavio', 'Morante-Palacios', email = 'octaviompa@gmail.com', role = c('cre', 'aut'))", "Description": "ShinyÉPICo is a graphical pipeline to analyze Illumina DNA\nmethylation arrays (450k or EPIC). It allows to calculate\ndifferentially methylated positions and differentially\nmethylated regions in a user-friendly interface. Moreover, it\nincludes several options to export the results and obtain files\nto perform downstream analysis.", "License": "AGPL-3 + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.1", "URL": "https://github.com/omorante/shiny_epico", "BugReports": "https://github.com/omorante/shiny_epico/issues", "VignetteBuilder": "knitr", "biocViews": "DifferentialMethylation,DNAMethylation,Microarray,Preprocessing,QualityControl", "Config/pak/sysreqs": "cmake make libmagick++-dev gsfonts libbz2-dev\nlibicu-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev\nlibssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:29 UTC", "RemoteUrl": "https://github.com/bioc/shinyepico", "RemoteRef": "HEAD", "RemoteSha": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 22:59:01 UTC", "User": "root" }, "Author": "Octavio Morante-Palacios [cre, aut]", "Maintainer": "Octavio Morante-Palacios ", "_user": "bioc", "_type": "src", "_file": "shinyepico_1.21.0.tar.gz", "_fileid": "https://r2.ropensci.org/37d00a7d0c59e8d136526d0791db32b05ca2130f9e161573734c34be4b800df0", "_filesize": 2160748, "_sha256": "37d00a7d0c59e8d136526d0791db32b05ca2130f9e161573734c34be4b800df0", "_expires": "2026-10-12T18:17:28.000Z", "_created": "2026-07-03T22:59:01.000Z", "_published": "2026-07-04T18:17:30.120Z", "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912", "_status": "success", "_upstream": "https://github.com/bioc/shinyepico", "_commit": { "id": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380869 }, "_maintainer": { "name": "Octavio Morante-Palacios", "email": "octaviompa@gmail.com", "login": "omorante", "twitter": "@octaviompa", "description": "Computational Biologist and Data Scientist ", "uuid": 24825834 }, "_distro": "resolute", "_jobs": [ { "job": 85155558346, "time": 649, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8075972958" }, { "job": 85155558436, "time": 722, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8075982846" }, { "job": 85155558558, "time": 731, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8075984183" }, { "job": 85155558432, "time": 317, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8075926693" }, { "job": 85155558363, "time": 358, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8075932278" }, { "job": 85155558328, "time": 736, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8075881387" }, { "job": 85155558424, "time": 673, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8075976069" }, { "job": 85155558420, "time": 649, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8075972870" }, { "job": 85155558460, "time": 581, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8075963898" }, { "job": 85155558390, "time": 634, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8075970859" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "DT", "version": ">= 0.15.0", "role": "Imports" }, { "package": "data.table", "version": ">= 1.13.0", "role": "Imports" }, { "package": "doParallel", "version": ">= 1.0.0", "role": "Imports" }, { "package": "dplyr", "version": ">= 1.0.9", "role": "Imports" }, { "package": "foreach", "version": ">= 1.5.0", "role": "Imports" }, { "package": "GenomicRanges", "version": ">= 1.38.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.3.0", "role": "Imports" }, { "package": "gplots", "version": ">= 3.0.0", "role": "Imports" }, { "package": "heatmaply", "version": ">= 1.1.0", "role": "Imports" }, { "package": "limma", "version": ">= 3.42.0", "role": "Imports" }, { "package": "minfi", "version": ">= 1.32.0", "role": "Imports" }, { "package": "plotly", "version": ">= 4.9.2", "role": "Imports" }, { "package": "reshape2", "version": ">= 1.4.0", "role": "Imports" }, { "package": "rlang", "version": ">= 1.0.2", "role": "Imports" }, { "package": "rmarkdown", "version": ">= 2.3.0", "role": "Imports" }, { "package": "rtracklayer", "version": ">= 1.46.0", "role": "Imports" }, { "package": "shiny", "version": ">= 1.5.0", "role": "Imports" }, { "package": "shinyWidgets", "version": ">= 0.5.0", "role": "Imports" }, { "package": "shinycssloaders", "version": ">= 0.3.0", "role": "Imports" }, { "package": "shinyjs", "version": ">= 1.1.0", "role": "Imports" }, { "package": "shinythemes", "version": ">= 1.1.0", "role": "Imports" }, { "package": "statmod", "version": ">= 1.4.0", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.2.0", "role": "Imports" }, { "package": "zip", "version": ">= 2.1.0", "role": "Imports" }, { "package": "knitr", "version": ">= 1.30.0", "role": "Suggests" }, { "package": "mCSEA", "version": ">= 1.10.0", "role": "Suggests" }, { "package": "IlluminaHumanMethylation450kanno.ilmn12.hg19", "role": "Suggests" }, { "package": "IlluminaHumanMethylation450kmanifest", "role": "Suggests" }, { "package": "IlluminaHumanMethylationEPICanno.ilm10b4.hg19", "role": "Suggests" }, { "package": "IlluminaHumanMethylationEPICmanifest", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "minfiData", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "differentialmethylation", "dnamethylation", "microarray", "preprocessing", "qualitycontrol" ], "_stars": 6, "_contributors": [ { "user": "omorante", "count": 211, "uuid": 24825834 }, { "user": "nturaga", "count": 6, "uuid": 2746443 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/omorante/shiny_epico", "_searchresults": 2, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/shinyepico.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/omorante/shinyepico", "_realowner": "bioc", "_cranurl": false, "_exports": [ "run_shinyepico" ], "_help": [ { "page": "shinyepico-package", "title": "shinyÉPICo: a graphical and interactive pipeline to analyze Illumina DNA Methylation Arrays", "topics": [ "shinyepico-package", "shinyepico" ] }, { "page": "run_shinyepico", "title": "Run Shiny ÉPICo!", "topics": [ "run_shinyepico" ] } ], "_readme": "https://github.com/bioc/shinyepico/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "assertthat", "base64", "base64enc", "beanplot", "BH", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocIO", "biocmake", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "bslib", "bumphunter", "ca", "cachem", "callr", "caTools", "cigarillo", "cli", "clipr", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "DelayedMatrixStats", "dendextend", "digest", "dir.expiry", "doParallel", "doRNG", "dplyr", "DT", "egg", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "gclus", "genefilter", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "GEOquery", "ggplot2", "glue", "gplots", "gridExtra", "gtable", "gtools", "h5mread", "HDF5Array", "heatmaply", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "httr2", "illuminaio", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mgcv", "mime", "minfi", "multtest", "nlme", "nor1mix", "openssl", "otel", "permute", "pillar", "pkgconfig", "plotly", "plyr", "png", "preprocessCore", "prettyunits", "processx", "progress", "promises", "ps", "purrr", "qap", "quadprog", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RCurl", "readr", "registry", "rentrez", "reshape", "reshape2", "restfulr", "rhdf5", "rhdf5filters", "Rhdf5lib", "Rhtslib", "rjson", "rlang", "rmarkdown", "rngtools", "Rsamtools", "RSQLite", "rtracklayer", "rvest", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scrime", "selectr", "Seqinfo", "seriation", "shiny", "shinycssloaders", "shinyjs", "shinythemes", "shinyWidgets", "siggenes", "snow", "sourcetools", "SparseArray", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "TSP", "tzdb", "utf8", "vctrs", "vegan", "viridis", "viridisLite", "vroom", "webshot", "withr", "xfun", "XML", "xml2", "xtable", "XVector", "yaml", "zip" ], "_vignettes": [ { "source": "shiny_epico.Rmd", "filename": "shiny_epico.html", "title": "shinyÉPICo: the user's guide", "author": "Octavio Morante-Palacios, Esteban Ballestar", "engine": "knitr::rmarkdown", "headings": [ "Introduction: What is ShinyÉPICo for?", "What do I need in order to use ShinyÉPICo?", "How can I install ShinyÉPICo?", "Dependencies and implementation", "ShinyÉPICo workflow", "Using ShinyÉPICO: an explanation of the options and an example with real data", "Data Import and Sample Selection", "Quality control charts", "Array Normalization", "Density plot", "Boxplot", "SNPs heatmap", "Sex prediction", "Exploratory analysis: PCA and Correlations", "Differentially Methylated Positions (DMP) calculation", "Model generation", "Contrasts calculation", "Heatmap customization", "DMPs Annotation", "Differentially Methylated Regions (DMR) calculation", "mCSEA options", "Single DMR plot", "Exporting results", "R Objects", "Filtered bed files", "Workflow Report", "Custom R Script", "Heatmap(s)", "Session info", "References" ], "created": "2020-03-27 00:04:05", "modified": "2020-11-20 14:06:35", "commits": 12 } ], "_score": 5.079181246047625, "_indexed": true, "_nocasepkg": "shinyepico", "_universes": [ "bioc", "omorante" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-07-03T23:09:30.000Z", "distro": "resolute", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/675b4c7b25fe05ad0af30c0acd3e72331adea724af28202f67d9cd19a7c68b82", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.6.1", "os": "linux", "version": "1.21.0", "date": "2026-07-03T23:09:38.000Z", "distro": "resolute", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/bb1bdb96c99c8292fa45f2971004849b70a9af78de6d2b4a75530129839d2fc1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-07-03T23:03:28.000Z", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/168068c9b88171e91e812ef729d120dcc6a402d1531354c9ac0736ecb8b49b71", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.6.1", "os": "mac", "version": "1.21.0", "date": "2026-07-03T23:04:00.000Z", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/c1e1763eead6e23d861ca766a314baac326906a0ffb9974c901c075edb0b58c8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-07-03T23:10:29.000Z", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/faa6b2836c36ca2a12311e1554b1cfa32eb860a52c33da34548fe4dc0331cffc", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-07-03T23:07:50.000Z", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/2e9f4bbacffcf22ef3dddfe1f396dc160dce8cdae0900161344c340bb98f7f2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-07-03T23:07:07.000Z", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/5cd0b0e2c529e6808c35cefbbf61baf23c9ac7c670ec63e5fbe3801fa30c60bd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" }, { "r": "4.6.1", "os": "win", "version": "1.21.0", "date": "2026-07-03T23:07:38.000Z", "commit": "f44c2c23041fbc38433d494ec47e90e9a24feb93", "fileid": "https://r2.ropensci.org/04cb02de69b137403d7bee885553d266ac17a72b3f5b25b81411630a4165eb90", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28686562912" } ] }