{ "_id": "6a169228acfb0bcc41d78ccd", "Package": "scpdata", "Type": "Package", "Title": "Single-Cell Proteomics Data Package", "Version": "1.19.2", "Authors@R": "c(person(\"Christophe\", \"Vanderaa\",\nemail = \"vanderaa.christophe@gmail.com\",\ncomment = c(ORCID = \"0000-0001-7443-5427\"),\nrole = c(\"aut\", \"cre\")),\nperson(\"Laurent\", \"Gatto\",\nemail = \"laurent.gatto@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-1520-2268\"),\nrole = \"aut\"),\nperson(\"Enes\", \"Ayar\",\nemail = \"enes.ayar@uclouvain.be\",\ncomment = c(ORCID = \"0000-0001-8881-9800\"),\nrole = \"dtc\"),\nperson(\"Samuel\", \"Grégoire\",\nemail = \"samuel.gregoire@uclouvain.be\",\ncomment = c(ORCID = \"0000-0002-0900-7677\"),\nrole = \"dtc\"))", "Description": "The package disseminates mass spectrometry (MS)-based\nsingle-cell proteomics (SCP) datasets. The data were collected\nfrom published work and formatted using the `scp` data\nstructure. The data sets contain quantitative information at\nspectrum, peptide and/or protein level for single cells or\nminute sample amounts.", "biocViews": "ExperimentData, ExpressionData, ExperimentHub,\nReproducibleResearch, MassSpectrometryData, Proteome,\nSingleCellData, PackageTypeData", "License": "GPL-2", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://uclouvain-cbio.r-universe.dev", "Date/Publication": "2026-04-27 14:43:09 UTC", "RemoteUrl": "https://github.com/uclouvain-cbio/scpdata", "RemoteRef": "HEAD", "RemoteSha": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 06:29:41 UTC", "User": "root" }, "Author": "Christophe Vanderaa [aut, cre] (ORCID:\n),\nLaurent Gatto [aut] (ORCID: ),\nEnes Ayar [dtc] (ORCID: ),\nSamuel Grégoire [dtc] (ORCID: )", "Maintainer": "Christophe Vanderaa ", "MD5sum": "e6d827a9d36c1783181d3fd97bf98c7b", "_user": "uclouvain-cbio", "_type": "src", "_file": "scpdata_1.19.2.tar.gz", "_fileid": "eab75838747ea85f9fb16585ecef58ce1d7b8a1a33a483439ad9b8634e879fca", "_filesize": 440497, "_sha256": "eab75838747ea85f9fb16585ecef58ce1d7b8a1a33a483439ad9b8634e879fca", "_created": "2026-05-27T06:29:41.000Z", "_published": "2026-05-27T06:41:44.832Z", "_distro": "noble", "_jobs": [ { "job": 78020565571, "time": 652, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7233604271" }, { "job": 78020565531, "time": 636, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7233600244" }, { "job": 78020565525, "time": 656, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7233604978" }, { "job": 78020565528, "time": 596, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7233589594" }, { "job": 78019931048, "time": 303, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7233428042" }, { "job": 78020565539, "time": 168, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7233471277" }, { "job": 78020565581, "time": 633, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7233599701" }, { "job": 78020565574, "time": 550, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7233577057" }, { "job": 78020565545, "time": 599, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7233590668" } ], "_buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/uclouvain-cbio/scpdata", "_commit": { "id": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "author": "Laurent Gatto ", "committer": "Laurent Gatto ", "message": "revert metadata for fixed data\n", "time": 1777300989 }, "_maintainer": { "name": "Christophe Vanderaa", "email": "vanderaa.christophe@gmail.com", "login": "cvanderaa", "orcid": "0000-0001-7443-5427", "description": "", "uuid": 43441105 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "QFeatures", "role": "Depends" }, { "package": "ExperimentHub", "role": "Depends" }, { "package": "utils", "role": "Imports" }, { "package": "AnnotationHub", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "scp", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "BiocCheck", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "uclouvain-cbio", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-17", "n": 4 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_topics": [ "experimentdata", "expressiondata", "experimenthub", "reproducibleresearch", "massspectrometrydata", "proteome", "singlecelldata", "packagetypedata" ], "_stars": 9, "_contributors": [ { "user": "cvanderaa", "count": 201, "uuid": 43441105 }, { "user": "lgatto", "count": 68, "uuid": 384198 }, { "user": "enessefaayar", "count": 37, "uuid": 92874184 }, { "user": "samgregoire", "count": 31, "uuid": 79509477 }, { "user": "hpages", "count": 10, "uuid": 8810451 }, { "user": "lshep", "count": 6, "uuid": 18724380 }, { "user": "leopoldguyot", "count": 6, "uuid": 104364239 }, { "user": "jwokaty", "count": 4, "uuid": 1744257 } ], "_userbio": { "uuid": 43893288, "type": "organization", "name": "Computational Biology and Bioinformatics at UCLouvain" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scpdata" }, "_devurl": "https://github.com/uclouvain-cbio/scpdata", "_searchresults": 40, "_rbuild": "4.6.0", "_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/scpdata.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "ai2025a", "brunner2022", "cong2020AC", "derks2022", "dou2019_boosting", "dou2019_lysates", "dou2019_mouse", "gregoire2023_mixCTRL", "guise2024", "hu2023_K562", "hu2023_oocyte", "khan2023", "krull2024", "leduc2022", "leduc2022_plexDIA", "leduc2022_pSCoPE", "liang2020_hela", "petrosius2023_AstralAML", "petrosius2023_mES", "schoof2021", "scpdata", "specht2019v2", "specht2019v3", "williams2020_lfq", "williams2020_tmt", "woo2022_lung", "woo2022_macrophage", "zhu2018MCP", "zhu2018NC_hela", "zhu2018NC_islets", "zhu2018NC_lysates", "zhu2019EL" ], "_help": [ { "page": "ai2025a", "title": "Ai et al., Cardiomyocytes Single Cell Proteomics, MCP (2025)", "topics": [ "ai2025a" ] }, { "page": "brunner2022", "title": "Brunner et al. 2022 (Mol. Syst. Biol.): cell cycle state study", "topics": [ "brunner2022" ] }, { "page": "cong2020AC", "title": "Cong et al. 2020 (Ana. Chem.): HeLa single cells", "topics": [ "cong2020AC" ] }, { "page": "derks2022", "title": "Derks et al. 2022 - plexDIA (Nat. Biotechnol.): PDAC vs melanoma cells vs monocytes", "topics": [ "derks2022" ] }, { "page": "dou2019_boosting", "title": "Dou et al. 2019 (Anal. Chem.): testing boosting ratios", "topics": [ "dou2019_boosting" ] }, { "page": "dou2019_lysates", "title": "Dou et al. 2019 (Anal. Chem.): HeLa lysates", "topics": [ "dou2019_lysates" ] }, { "page": "dou2019_mouse", "title": "Dou et al. 2019 (Anal. Chem.): murine cell lines", "topics": [ "dou2019_mouse" ] }, { "page": "gregoire2023_mixCTRL", "title": "Grégoire et al. 2023 - mixCTRL (arXiv): benchmark using monocytes/macrophages", "topics": [ "gregoire2023_mixCTRL" ] }, { "page": "guise2024", "title": "Guise et al. 2020 (Cell Rep.): postmortem ALS spinal moto neurons", "topics": [ "guise2024" ] }, { "page": "hu2023_K562", "title": "Hu et al, 2023 (The Journal of Physical Chemistry B): Correlated protein modules", "topics": [ "hu2023", "hu2023_K562", "hu2023_oocyte" ] }, { "page": "khan2023", "title": "Khan et al, 2023 (biorRxiv): Epithelial–Mesenchymal Transition", "topics": [ "khan2023" ] }, { "page": "krull2024", "title": "Krull et al, 2024 (Nature Communications): IFN-gamma response", "topics": [ "krull2024" ] }, { "page": "leduc2022", "title": "Deprecated leduc2022 dataset", "topics": [ "leduc2022" ] }, { "page": "leduc2022_plexDIA", "title": "Leduc et al. 2022 - plexDIA (biorRxiv): melanoma cells", "topics": [ "leduc2022_plexDIA" ] }, { "page": "leduc2022_pSCoPE", "title": "Leduc et al. 2022 - pSCoPE (biorRxiv): melanoma cells vs monocytes", "topics": [ "leduc2022_pSCoPE" ] }, { "page": "liang2020_hela", "title": "Liang et al. 2020 (Anal. Chem.): HeLa cells (MaxQuant preprocessing)", "topics": [ "liang2020_hela" ] }, { "page": "petrosius2023_AstralAML", "title": "Petrosius et al. 2023 (bioRxiv): AML hierarchy on Astral.", "topics": [ "petrosius2023_AstralAML" ] }, { "page": "petrosius2023_mES", "title": "Petrosius et al, 2023 (Nat. Comm.): Mouse embryonic stem cell (mESC) in different culture conditions", "topics": [ "petrosius2023_mES" ] }, { "page": "schoof2021", "title": "Schoof et al. 2021 (Nat. Comm.): acute myeloid leukemia differentiation", "topics": [ "schoof2021" ] }, { "page": "scpdata", "title": "Single-Cell Proteomics Data Package", "topics": [ "scpdata-package", "scpdata" ] }, { "page": "specht2019v2", "title": "Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 2)", "topics": [ "specht2019v2" ] }, { "page": "specht2019v3", "title": "Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 3)", "topics": [ "specht2019v3" ] }, { "page": "williams2020_lfq", "title": "Williams et al. 2020 (Anal. Chem.): MCF10A cell line", "topics": [ "williams2020_lfq" ] }, { "page": "williams2020_tmt", "title": "Williams et al. 2020 (Anal. Chem.): 3 AML cell line", "topics": [ "williams2020_tmt" ] }, { "page": "woo2022_lung", "title": "Woo et al. 2022 (Cell Syst.): 26 primary human lung cells", "topics": [ "woo2022_lung" ] }, { "page": "woo2022_macrophage", "title": "Woo et al. 2022 (Cell Syst.): LPS-treated macrophages", "topics": [ "woo2022_macrophage" ] }, { "page": "wu2026", "title": "Wu et al., 2026 (Nature Biotechnology): single-cell proteomic landscape of the developing human brain", "topics": [ "wu2026" ] }, { "page": "zhu2018MCP", "title": "Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser dissections", "topics": [ "zhu2018MCP" ] }, { "page": "zhu2018NC_hela", "title": "Zhu et al. 2018 (Nat. Comm.): HeLa titration", "topics": [ "zhu2018NC_hela" ] }, { "page": "zhu2018NC_islets", "title": "Zhu et al. 2018 (Nat. Comm.): human pancreatic islets", "topics": [ "zhu2018NC_islets" ] }, { "page": "zhu2018NC_lysates", "title": "Zhu et al. 2018 (Nat. Comm.): HeLa lysates", "topics": [ "zhu2018NC_lysates" ] }, { "page": "zhu2019EL", "title": "Zhu et al. 2019 (eLife): chicken utricle cells", "topics": [ "zhu2019EL" ] } ], "_readme": "https://github.com/uclouvain-cbio/scpdata/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "AnnotationHub", "askpass", "base64enc", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "BiocVersion", "Biostrings", "bit", "bit64", "blob", "bslib", "cachem", "cli", "clue", "cluster", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "digest", "dplyr", "evaluate", "ExperimentHub", "farver", "fastmap", "filelock", "fontawesome", "fs", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "httr2", "igraph", "IRanges", "isoband", "jquerylib", "jsonlite", "KEGGREST", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "MsCoreUtils", "MultiAssayExperiment", "openssl", "otel", "pillar", "pkgconfig", "plotly", "plyr", "png", "promises", "ProtGenerics", "purrr", "QFeatures", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "rlang", "rmarkdown", "RSQLite", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "SingleCellExperiment", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "withr", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "contribution_guidelines.Rmd", "filename": "contribution_guidelines.html", "title": "Contribution guidelines", "author": "Christophe Vanderaa, Laurent Gatto", "engine": "knitr::rmarkdown", "headings": [ "Getting started with GitHub", "What do we expect?", "QFeatures object", "Feature data", "Sample annotations", "Experiment description", "Data source information", "Folder structure", "inst/scripts/", "R/", "man/", "Workflow", "1. Collect data", "2. Create the QFeatures object", "3. Document the dataset", "4. Update metadata", "5. Create a pull request", "6. Almost done!" ], "created": "2024-02-15 13:50:44", "modified": "2024-03-11 13:01:24", "commits": 2 }, { "source": "scpdata.Rmd", "filename": "scpdata.html", "title": "Single Cell Proteomics data sets", "author": "Laurent Gatto, Christophe Vanderaa", "engine": "knitr::rmarkdown", "headings": [ "The scpdata package", "Load data from ExperimentHub", "Data sets information", "Data manipulation", "Session information", "License" ], "created": "2019-10-15 14:19:00", "modified": "2024-02-15 13:50:44", "commits": 18 } ], "_score": 5.878521795501206, "_indexed": true, "_nocasepkg": "scpdata", "_universes": [ "uclouvain-cbio", "cvanderaa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.2", "date": "2026-05-27T06:33:02.000Z", "distro": "noble", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "adf18a14306db12b13302d5b94e297076e26fb1a4e61e44c425a462b2e3451f0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.6.0", "os": "linux", "version": "1.19.2", "date": "2026-05-27T06:32:54.000Z", "distro": "noble", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "2d30f04deec3b6b453638de75938933d3b2067a10def5ca33380ddb6682e39ec", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.5.3", "os": "mac", "version": "1.19.2", "date": "2026-05-27T06:32:02.000Z", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "0b2488efdc828857b521b326079ff0943f350687d9b27e30d540b905d0572a5b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.6.0", "os": "mac", "version": "1.19.2", "date": "2026-05-27T06:31:50.000Z", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "d051a7c4c66f557cc616f8829b1ecb5d616bd579431a021e980387658a1421f9", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.2", "date": "2026-05-27T06:33:03.000Z", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "a595080a5764733d57913001617599d3ed5803162ebde3a968ccf4fd08dda413", "status": "success", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.7.0", "os": "win", "version": "1.19.2", "date": "2026-05-27T06:32:14.000Z", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "a1fc8292f4e76327de7cb7b4ab05f54f12fae7cacf23419e1d3abf303a2bdb9e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.5.3", "os": "win", "version": "1.19.2", "date": "2026-05-27T06:31:37.000Z", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "cde40d552b54e302def9c91d3606812a0ce621ae668a1b1482c6ab3191a6337d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" }, { "r": "4.6.0", "os": "win", "version": "1.19.2", "date": "2026-05-27T06:32:02.000Z", "commit": "c80a5e17d05fd110f69f091ada3b4f4a33f627a1", "fileid": "b5a495ee748c4b134a9cb35cd9fc97e595a555c515c8fb7ba2c512a033010db5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/uclouvain-cbio/actions/runs/26494654807" } ] }