{ "_id": "6a13f02cacfb0bcc41d301f1", "Package": "ExpressionAtlas", "Version": "2.4.0", "Date": "2025/09/01", "Title": "Download datasets from EMBL-EBI Expression Atlas", "Authors@R": "c(person(given = \"Maria\",\nfamily = \"Keays\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-2034-601X\")\n),\nperson(given = \"Pedro\",\nfamily = \"Madrigal\",\nrole = c(\"aut\"),\nemail = \"pmadrigal@ebi.ac.uk\",\ncomment = c(ORCID = \"0000-0003-1959-8199\")\n),\nperson(given = \"Anil\",\nfamily = \"Thanki\",\nrole = c(\"cre\"),\nemail = \"anilthanki@ebi.ac.uk\",\ncomment = c(ORCID = \"0000-0002-8941-444X\")\n)\n)", "Description": "This package is for searching for datasets in EMBL-EBI\nExpression Atlas, and downloading them into R for further\nanalysis. Each Expression Atlas dataset is represented as a\nSimpleList object with one element per platform. Sequencing\ndata is contained in a SummarizedExperiment object, while\nmicroarray data is contained in an ExpressionSet or MAList\nobject.", "biocViews": "ExpressionData, ExperimentData, SequencingData,\nMicroarrayData, ArrayExpress", "VignetteBuilder": "knitr", "Collate": "functions.R", "License": "GPL (>= 3)", "LazyLoad": "yes", "NeedsCompilation": "no", "Config/pak/sysreqs": "cmake make libuv1-dev libxml2-dev libssl-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:42:41 UTC", "RemoteUrl": "https://github.com/bioc/ExpressionAtlas", "RemoteRef": "RELEASE_3_23", "RemoteSha": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "Packaged": { "Date": "2026-05-25 06:39:32 UTC", "User": "root" }, "Author": "Maria Keays [aut] (ORCID: ),\nPedro Madrigal [aut] (ORCID: ),\nAnil Thanki [cre] (ORCID: )", "Maintainer": "Anil Thanki ", "MD5sum": "e8848ae7859980613b93265ba3e8591e", "_user": "bioc-release", "_type": "src", "_file": "ExpressionAtlas_2.4.0.tar.gz", "_fileid": "711f6929a3dec9661f8f616436c57bc81e7322d5ca4ae71d38c0c74425e6b333", "_filesize": 202841, "_sha256": "711f6929a3dec9661f8f616436c57bc81e7322d5ca4ae71d38c0c74425e6b333", "_created": "2026-05-25T06:39:32.000Z", "_published": "2026-05-25T06:46:04.377Z", "_jobs": [ { "job": 77668172844, "time": 178, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7193050222" }, { "job": 77668172851, "time": 345, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7193087758" }, { "job": 77668172830, "time": 348, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7193088282" }, { "job": 77668172847, "time": 201, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7193055423" }, { "job": 77668172837, "time": 224, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7193060320" }, { "job": 77667658046, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7193008099" }, { "job": 77668172849, "time": 110, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7193034811" }, { "job": 77668172922, "time": 228, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7193061199" }, { "job": 77668172914, "time": 213, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7193057890" }, { "job": 77668172898, "time": 218, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7193058973" } ], "_bioccheck": { "error": 2, "warning": 2, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/ExpressionAtlas", "_commit": { "id": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "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": 1777380161 }, "_maintainer": { "name": "Anil Thanki", "email": "anilthanki@ebi.ac.uk", "login": "anilthanki", "mastodon": "@anilthanki@mastodon.social", "bluesky": "@anilthanki.bsky.social", "linkedin": "in/anilthanki", "twitter": "@anilthanki", "description": "", "uuid": 3940626, "orcid": "0000-0002-8941-444X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "Biobase", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "S4Vectors", "role": "Depends" }, { "package": "xml2", "role": "Depends" }, { "package": "RCurl", "role": "Depends" }, { "package": "jsonlite", "role": "Depends" }, { "package": "BiocStyle", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "XML", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-37", "n": 1 }, { "week": "2025-38", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "2.5.0", "bioc": "3.24" }, { "branch": "release", "version": "2.4.0", "bioc": "3.23" } ], "_topics": [ "expressiondata", "experimentdata", "sequencingdata", "microarraydata", "arrayexpress" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 414, "source": "https://www.bioconductor.org/packages/stats/bioc/ExpressionAtlas" }, "_mentions": 7, "_searchresults": 24, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/ExpressionAtlas.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_homeurl": "https://github.com/ebi-gene-expression-group/bioconductor-expressionatlas", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getAtlasData", "getAtlasExperiment", "searchAtlasExperiments" ], "_datasets": [ { "name": "allExps", "title": "A SimpleList containing some dummy Expression Atlas datasets", "object": "allExps", "file": "allExps.rda", "class": [ "SimpleList" ], "fields": [], "table": false, "tojson": false }, { "name": "atlasRes", "title": "A DataFrame listing some Expression Atlas experiments", "object": "atlasRes", "file": "atlasRes.rda", "class": [ "DFrame" ], "fields": [], "table": false, "tojson": false }, { "name": "rnaseqExps", "title": "A SimpleList containing a dummy RNA-seq Expression Atlas dataset", "object": "rnaseqExps", "file": "rnaseqExps.rda", "class": [ "SimpleList" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "allExps", "title": "A SimpleList containing some dummy Expression Atlas datasets", "topics": [ "allExps" ] }, { "page": "atlasRes", "title": "A DataFrame listing some Expression Atlas experiments", "topics": [ "atlasRes" ] }, { "page": "getAtlasData", "title": "Download data from multiple Expression Atlas experiments", "topics": [ "getAtlasData" ] }, { "page": "getAtlasExperiment", "title": "Download data for an Expression Atlas experiment", "topics": [ "getAtlasExperiment" ] }, { "page": "rnaseqExps", "title": "A SimpleList containing a dummy RNA-seq Expression Atlas dataset", "topics": [ "rnaseqExps" ] }, { "page": "searchAtlasExperiments", "title": "Search for Expression Atlas experiments", "topics": [ "searchAtlasExperiments" ] } ], "_rundeps": [ "abind", "askpass", "base64enc", "Biobase", "BiocGenerics", "BiocManager", "BiocStyle", "bitops", "bookdown", "bslib", "cachem", "cli", "curl", "DelayedArray", "digest", "evaluate", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "highr", "htmltools", "httr", "IRanges", "jquerylib", "jsonlite", "knitr", "lattice", "lifecycle", "limma", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "R6", "rappdirs", "RCurl", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "sass", "Seqinfo", "SparseArray", "statmod", "SummarizedExperiment", "sys", "tinytex", "xfun", "XML", "xml2", "XVector", "yaml" ], "_vignettes": [ { "source": "ExpressionAtlas.Rmd", "filename": "ExpressionAtlas.html", "title": "ExpressionAtlas package vignette", "author": "Maria Keays", "engine": "knitr::rmarkdown", "headings": [ "Expression Atlas", "Searching and downloading Expression Atlas data", "Searching", "Downloading the data", "RNA-seq experiment summaries", "Single-channel microarray experiments", "Downloading a single Expression Atlas experiment summary" ], "created": "2016-02-22 18:03:39", "modified": "2022-10-21 11:41:53", "commits": 4 } ], "_score": 4.827369273053825, "_indexed": false, "_nocasepkg": "expressionatlas", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/ExpressionAtlas", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.4.0", "date": "2026-05-25T06:43:01.000Z", "distro": "noble", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "52a346d1f194a5aefe6136310c65481b8046c4f4beadb40e60474304367bd091", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.6.0", "os": "linux", "version": "2.4.0", "date": "2026-05-25T06:42:28.000Z", "distro": "noble", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "eaaa238875501fcf72ece2b52878ed550e79e7e431c4872144d38727397897b4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.5.3", "os": "mac", "version": "2.4.0", "date": "2026-05-25T06:41:22.000Z", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "e7fc498f5de950859bb98f5973374a1636de39b431e3a8d7591bbca19e7f0b97", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.6.0", "os": "mac", "version": "2.4.0", "date": "2026-05-25T06:41:28.000Z", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "cd119235a012264114dbe77b304e662787aa30a01a26ca99e06f196a05dfc626", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.6.0", "os": "wasm", "version": "2.4.0", "date": "2026-05-25T06:41:50.000Z", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "4897a207cc630550b018898eceb52e1dc87e16362e2800acaf0fcc948bfde450", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.7.0", "os": "win", "version": "2.4.0", "date": "2026-05-25T06:41:00.000Z", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "4cecf863f28253ad26751b9ebb7fd09ac5157bc56f5f405c54b5fe75f926890f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.5.3", "os": "win", "version": "2.4.0", "date": "2026-05-25T06:40:57.000Z", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "48dfb06bd6470624cf9d356f1e16bb40a870b3ccc963d044eb16bad899a76b87", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" }, { "r": "4.6.0", "os": "win", "version": "2.4.0", "date": "2026-05-25T06:41:05.000Z", "commit": "5f9865f07d2bcf52ab967664b4ea96f2b78e93ed", "fileid": "568a4f2d360751107ae11f31a834d205b8502df0c739c03ee286c25e26091dac", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26386992568" } ] }