{ "_id": "6ad9c8e0c230b829876fdef1", "Package": "SEtools", "Type": "Package", "Title": "SEtools: tools for working with SummarizedExperiment", "Version": "1.27.0", "Authors@R": "person(\"Pierre-Luc\", \"Germain\", email=\"pierre-luc.germain@hest.ethz.ch\", role=c(\"cre\",\"aut\"), comment=c(ORCID=\"0000-0003-3418-4218\"))", "Description": "This includes a set of convenience functions for working\nwith the SummarizedExperiment class. Note that plotting\nfunctions historically in this package have been moved to the\nsechm package (see vignette for details).", "biocViews": "GeneExpression", "VignetteBuilder": "knitr", "License": "GPL", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "BugReports": "https://github.com/plger/SEtools", "Config/pak/sysreqs": "libicu-dev libpng-dev libxml2-dev libssl-dev perl\nlibnode-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:50:54 UTC", "RemoteUrl": "https://github.com/bioc/SEtools", "RemoteRef": "HEAD", "RemoteSha": "67898208e54f2d58b682dd58d6f64fee3a025670", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-22 08:16:57 UTC", "User": "root" }, "Author": "Pierre-Luc Germain [cre, aut] (ORCID:\n)", "Maintainer": "Pierre-Luc Germain ", "_user": "bioc", "_type": "src", "_file": "SEtools_1.27.0.tar.gz", "_fileid": "https://r2.ropensci.org/3f902ffd5f9d000f52065045b95cfb04fde1023d1ff0b756c94c24a678f9eb2e", "_filesize": 447696, "_sha256": "3f902ffd5f9d000f52065045b95cfb04fde1023d1ff0b756c94c24a678f9eb2e", "_expires": "2027-01-30T08:27:10.000Z", "_created": "2026-10-22T08:16:57.000Z", "_published": "2026-10-22T08:27:12.427Z", "_upstream": "https://github.com/bioc/SEtools", "_status": "success", "_maintainer": { "name": "Pierre-Luc Germain", "email": "pierre-luc.germain@hest.ethz.ch", "login": "plger", "orcid": "0000-0003-3418-4218", "description": "like sailors who on the open sea must reconstruct their ship but are never able to start afresh from the bottom...", "uuid": 9786697 }, "_jobs": [ { "job": 119716731013, "time": 304, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "12411214940" }, { "job": 119716730941, "time": 399, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12411499358" }, { "job": 119716731056, "time": 549, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12411857490" }, { "job": 119716731025, "time": 238, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "12412110992" }, { "job": 119716731100, "time": 243, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "12412325362" }, { "job": 119713578507, "time": 458, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12411662387" }, { "job": 119716730931, "time": 337, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12412006726" }, { "job": 119716731062, "time": 263, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "12411712967" }, { "job": 119716730996, "time": 260, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "12411434256" }, { "job": 119716730980, "time": 439, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "12412156491" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351", "_commit": { "id": "67898208e54f2d58b682dd58d6f64fee3a025670", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380654 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "sechm", "role": "Depends" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "openxlsx", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "circlize", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.27.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.26.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "geneexpression" ], "_stars": 4, "_contributors": [ { "user": "plger", "count": 173, "uuid": 9786697 }, { "user": "nturaga", "count": 12, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "hpages", "count": 1, "uuid": 8810451 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 479, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 503, "source": "https://www.bioconductor.org/packages/stats/bioc/SEtools" }, "_devurl": "https://github.com/plger/setools", "_searchresults": 101, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/SEtools.html" ], "_homeurl": "https://github.com/plger/setools", "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggSE", "castSE", "flattenPB", "log2FC", "mergeSEs", "resetAllSEtoolsOptions", "se2xls", "sehm", "svacor" ], "_datasets": [ { "name": "SE", "title": "Example dataset", "object": "SE", "file": "SE.RData", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "aggSE", "title": "aggSE", "topics": [ "aggSE" ] }, { "page": "castSE", "title": "castSE", "topics": [ "castSE" ] }, { "page": "data", "title": "Example dataset", "topics": [ "data", "SE" ] }, { "page": "flattenPB", "title": "flattenPB", "topics": [ "flattenPB" ] }, { "page": "log2FC", "title": "log2FC", "topics": [ "log2FC" ] }, { "page": "mergeSEs", "title": "mergeSEs", "topics": [ "mergeSEs" ] }, { "page": "resetAllSEtoolsOptions", "title": "resetAllSEtoolsOptions", "topics": [ "resetAllSEtoolsOptions" ] }, { "page": "se2xls", "title": "se2xlsx", "topics": [ "se2xls" ] }, { "page": "sehm", "title": "sehm", "topics": [ "sehm" ] }, { "page": "svacor", "title": "svacor", "topics": [ "svacor" ] } ], "_readme": "https://github.com/bioc/SEtools/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "ca", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "data.table", "DBI", "DelayedArray", "DESeq2", "digest", "doParallel", "edgeR", "farver", "fastmap", "foreach", "formatR", "futile.logger", "futile.options", "gclus", "genefilter", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "GlobalOptions", "glue", "gtable", "httr", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mgcv", "mime", "nlme", "openssl", "openxlsx", "pheatmap", "pkgconfig", "png", "qap", "R6", "randomcoloR", "RColorBrewer", "Rcpp", "RcppArmadillo", "registry", "rjson", "rlang", "RSQLite", "Rtsne", "S4Arrays", "S4Vectors", "S7", "scales", "sechm", "Seqinfo", "seriation", "shape", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sva", "sys", "TSP", "V8", "vctrs", "viridisLite", "withr", "XML", "xtable", "XVector", "zip" ], "_vignettes": [ { "source": "SEtools.Rmd", "filename": "SEtools.html", "title": "SEtools", "author": "Pierre-Luc Germain", "engine": "knitr::rmarkdown", "headings": [ "Getting started", "Package installation", "Example data", "Merging and aggregating SEs", "Merging by rowData columns", "Aggregating a SE", "Other convenience functions", "Session info" ], "created": "2019-06-15 16:27:36", "modified": "2022-11-27 13:27:17", "commits": 20 } ], "_score": 6.083502619830267, "_indexed": true, "_nocasepkg": "setools", "_universes": [ "bioc", "plger" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-10-22T08:21:17.000Z", "distro": "resolute", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/6eedf18e2baa9a6d39ae8bb32cf62f33a6a78d72dbfc7f5359b06952f9199f8a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.6.1", "os": "linux", "version": "1.27.0", "date": "2026-10-22T08:23:47.000Z", "distro": "resolute", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/1861983dd676b5156444113669ff2aa108e79a6c5b767349048e7af71d70dbc5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-10-22T08:19:12.000Z", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/83c58d47ca1ba9f5bfdb159b19a53c36390ccc20ab1cb9db8d71158e8e1fc97e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.6.1", "os": "mac", "version": "1.27.0", "date": "2026-10-22T08:19:23.000Z", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/72992c06e4197b031338a9c83d6991a00bdb0898446e36a933a96e868551cf2d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-10-22T08:23:10.000Z", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/8d41084731dafcf5252406707a7e4689cb5d49c3d2a2b7109c4fbcf20c7d06d3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-10-22T08:18:52.000Z", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/9bed28683637b848a9676c486a2649224870324feea4abc267b7a4ffb11f786f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-10-22T08:19:12.000Z", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/ba86cb495c09d91535b10b249dc7587e3b4907516c282a51e6a7deb344fded3a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" }, { "r": "4.6.1", "os": "win", "version": "1.27.0", "date": "2026-10-22T08:22:08.000Z", "commit": "67898208e54f2d58b682dd58d6f64fee3a025670", "fileid": "https://r2.ropensci.org/01e263a64c902984c72ef66280ef2bb2732d54cb8d859c5af1d145bd2ed87348", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/39745691351" } ] }