{ "_id": "6a101516acfb0bcc41c83e1e", "Package": "seahtrue", "Type": "Package", "Title": "Seahtrue revives XF data for structured data analysis", "Version": "1.7.0", "Authors@R": "c(\nperson(\"Vincent\", \"de Boer\",\nemail = \"vincent.deboer@wur.nl\",\nrole = c(\"cre\", \"aut\"),\ncomment=c(ORCID=\"0000-0001-9928-1698\")),\nperson(\"Gerwin\", \"Smits\", role = c(\"aut\")),\nperson(\"Xiang\", \"Zhang\", role = c(\"aut\"))\n)", "Description": "Seahtrue organizes oxygen consumption and extracellular\nacidification analysis data from experiments performed on an XF\nanalyzer into structured nested tibbles.This allows for\ndetailed processing of raw data and advanced data visualization\nand statistics. Seahtrue introduces an open and reproducible\nway to analyze these XF experiments. It uses file paths to\n.xlsx files. These .xlsx files are supplied by the userand are\ngenerated by the user in the Wave software from Agilent from\nthe assay result files (.asyr). The .xlsx file contains\ndifferent sheets of important data for the experiment; 1. Assay\nInformation - Details about how the experiment was set up. 2.\nRate Data - Information about the OCR and ECAR rates. 3. Raw\nData - The original raw data collected during the experiment.\n4. Calibration Data - Data related to calibrating the\ninstrument. Seahtrue focuses on getting the specific data\nneeded for analysis. Once this data is extracted, it is\nprepared for calculations through preprocessing. To make sure\neverything is accurate, both the initial data and the\npreprocessed data go through thorough checks.", "biocViews": "CellBasedAssays, FunctionalPrediction, DataRepresentation,\nDataImport, CellBiology, Cheminformatics, Metabolomics,\nMicrotitrePlateAssay, Visualization, QualityControl,\nBatchEffect, ExperimentalDesign, Preprocessing, GO", "License": "Artistic-2.0", "Encoding": "UTF-8", "LazyData": "false", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "URL": "https://vcjdeboer.github.io/seahtrue/", "BugReports": "https://vcjdeboer.github.io/seahtrue/issues", "Config/pak/sysreqs": "libicu-dev libx11-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:03:30 UTC", "RemoteUrl": "https://github.com/bioc/seahtrue", "RemoteRef": "HEAD", "RemoteSha": "98febcffc151698b961f2016926855bb407d6e6a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-14 09:46:23 UTC", "User": "root" }, "Author": "Vincent de Boer [cre, aut] (ORCID:\n),\nGerwin Smits [aut],\nXiang Zhang [aut]", "Maintainer": "Vincent de Boer ", "MD5sum": "eca984f35738083d068bb1da1441ba9a", "_user": "bioc", "_type": "src", "_file": "seahtrue_1.7.0.tar.gz", "_fileid": "05b255ff10599a3bca14026553a83cd1e70eead82f8e80742d17c85ebb5156b7", "_filesize": 3299371, "_sha256": "05b255ff10599a3bca14026553a83cd1e70eead82f8e80742d17c85ebb5156b7", "_created": "2026-05-14T09:46:23.000Z", "_published": "2026-05-22T08:34:30.570Z", "_jobs": [ { "job": 77344561858, "time": 158, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "6991664700" }, { "job": 77344561623, "time": 324, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6991713000" }, { "job": 77344561564, "time": 363, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6991724130" }, { "job": 77344561774, "time": 196, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6991673371" }, { "job": 77344561386, "time": 337, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7011024049" }, { "job": 77344560829, "time": 312, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6991619067" }, { "job": 77344560935, "time": 125, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156255859" }, { "job": 77344561526, "time": 364, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6991722504" }, { "job": 77344561884, "time": 293, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6991702234" }, { "job": 77344562024, "time": 284, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6991699288" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 5 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/seahtrue", "_commit": { "id": "98febcffc151698b961f2016926855bb407d6e6a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381410 }, "_maintainer": { "name": "Vincent de Boer", "email": "vincent.deboer@wur.nl", "login": "vcjdeboer", "bluesky": "@vcjdeboer.bsky.social", "linkedin": "in/vincent-cj-de-boer-22283b18", "orcid": "0000-0001-9928-1698", "uuid": 75069552 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "dplyr", "version": ">= 1.1.2", "role": "Imports" }, { "package": "readxl", "version": ">= 1.4.1", "role": "Imports" }, { "package": "logger", "version": ">= 0.2.2", "role": "Imports" }, { "package": "tidyxl", "version": ">= 1.0.8", "role": "Imports" }, { "package": "purrr", "version": ">= 0.3.5", "role": "Imports" }, { "package": "tidyr", "version": ">= 1.3.0", "role": "Imports" }, { "package": "lubridate", "version": ">= 1.8.0", "role": "Imports" }, { "package": "stringr", "version": ">= 1.4.1", "role": "Imports" }, { "package": "tibble", "version": ">= 3.1.8", "role": "Imports" }, { "package": "validate", "version": ">= 1.1.1", "role": "Imports" }, { "package": "rlang", "version": ">= 1.0.0", "role": "Imports" }, { "package": "glue", "version": ">= 1.6.2", "role": "Imports" }, { "package": "cli", "version": ">= 3.4.1", "role": "Imports" }, { "package": "janitor", "version": ">= 2.2.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.5.0", "role": "Imports" }, { "package": "RColorBrewer", "version": ">= 1.1.3", "role": "Imports" }, { "package": "colorspace", "version": ">= 2.1.0", "role": "Imports" }, { "package": "forcats", "version": ">= 1.0.0", "role": "Imports" }, { "package": "ggridges", "version": ">= 0.5.6", "role": "Imports" }, { "package": "readr", "version": ">= 2.1.5", "role": "Imports" }, { "package": "scales", "version": ">= 1.3.0", "role": "Imports" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "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": "1.7.0", "bioc": "3.24" }, { "branch": "release", "version": "1.6.0", "bioc": "3.23" } ], "_topics": [ "cellbasedassays", "functionalprediction", "datarepresentation", "dataimport", "cellbiology", "cheminformatics", "metabolomics", "microtitreplateassay", "visualization", "qualitycontrol", "batcheffect", "experimentaldesign", "preprocessing", "go" ], "_stars": 2, "_contributors": [ { "user": "vcjdeboer", "count": 219, "uuid": 75069552 }, { "user": "smitsg", "count": 110, "uuid": 25744196 }, { "user": "pabrod", "count": 3, "uuid": 7677614 }, { "user": "jwokaty", "count": 1, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 238, "source": "https://www.bioconductor.org/packages/stats/bioc/seahtrue" }, "_devurl": "https://github.com/vcjdeboer/seahtrue", "_searchresults": 4, "_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/seahtrue.html", "manual.pdf" ], "_homeurl": "https://github.com/vcjdeboer/seahtrue", "_realowner": "bioc", "_cranurl": false, "_exports": [ "glue_xfplates", "revive_xfplate", "sketch_assimilate_rate", "sketch_assimilate_raw", "sketch_plate", "sketch_rate" ], "_datasets": [ { "name": "revive_output_donor_A", "title": "Dataset PBMC donor A", "object": "revive_output_donor_A", "file": "revive_output_donor_A.rda", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "plate_id", "filepath_seahorse", "date_run", "date_processed", "assay_info", "injection_info", "raw_data", "rate_data", "validation_output" ], "rows": 1, "table": false, "tojson": false } ], "_help": [ { "page": "glue_xfplates", "title": "Glueing mulltiple plates from a folder", "topics": [ "glue_xfplates" ] }, { "page": "revive_output_donor_A", "title": "Dataset PBMC donor A", "topics": [ "revive_output_donor_A" ] }, { "page": "revive_xfplate", "title": "Running the read, preprocess and validate", "topics": [ "revive_xfplate" ] }, { "page": "sketch_assimilate_rate", "title": "Combine multiple revived xf plates into one plot for rate data", "topics": [ "sketch_assimilate_rate" ] }, { "page": "sketch_assimilate_raw", "title": "Combine multiple revived xf plates into one plot for raw data", "topics": [ "sketch_assimilate_raw" ] }, { "page": "sketch_plate", "title": "Make an overview of plate layout, with colored groups", "topics": [ "sketch_plate" ] }, { "page": "sketch_rate", "title": "Generate a plot for the rate data", "topics": [ "sketch_rate" ] } ], "_pkglogo": "https://github.com/bioc/seahtrue/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/seahtrue/raw/HEAD/README.md", "_rundeps": [ "bit", "bit64", "cellranger", "cli", "clipr", "colorspace", "cpp11", "crayon", "dplyr", "farver", "forcats", "generics", "ggplot2", "ggridges", "glue", "gtable", "hms", "isoband", "janitor", "labeling", "lifecycle", "logger", "lubridate", "magrittr", "pillar", "piton", "pkgconfig", "prettyunits", "progress", "purrr", "R6", "RColorBrewer", "Rcpp", "readr", "readxl", "rematch", "rlang", "S7", "scales", "settings", "snakecase", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tidyxl", "timechange", "tzdb", "utf8", "validate", "vctrs", "viridisLite", "vroom", "withr", "yaml" ], "_vignettes": [ { "source": "seahtrue.Rmd", "filename": "seahtrue.html", "title": "Introduction to Seahtrue", "author": "Vincent C. J. de Boer, Gerwin Smits, Xiang Zhang", "engine": "knitr::rmarkdown", "headings": [ "Seahtrue overview", "Extracellular flux analysis scientific primer", "Resources", "Seahtrue", "Inspect the seahtrue data", "Rate data", "Raw data", "Assay info", "Injection info", "Session info" ], "created": "2024-03-07 09:21:34", "modified": "2024-07-19 12:05:36", "commits": 16 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "seahtrue", "_universes": [ "bioc", "vcjdeboer" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.0", "date": "2026-05-14T09:49:12.000Z", "distro": "noble", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "fc453c8a653aa37b4d4fd0bc6c99b69a89bb4e3c2244b1ecb53b55979df555a9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.6.0", "os": "linux", "version": "1.7.0", "date": "2026-05-14T09:49:53.000Z", "distro": "noble", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "4b1fdd749a2528fb3a849eee48145aebaf1c44d8aa110e6641da0b27998d2bed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0", "date": "2026-05-14T09:48:01.000Z", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "18c911253383ccc3ef9f04923ff1ea43f87072f906845ab18295418446c2d36e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.6.0", "os": "mac", "version": "1.7.0", "date": "2026-05-15T05:53:53.000Z", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "e034eea83be0dbec6a4d5c50c319386efd23ee6ad3a5c0380468b285ebcbca83", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.7.0", "os": "win", "version": "1.7.0", "date": "2026-05-14T09:47:47.000Z", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "c158629f9071aef378a35c06875efd7e81cae87768805903e1dcfce72b04196b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.5.3", "os": "win", "version": "1.7.0", "date": "2026-05-14T09:47:45.000Z", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "26690c43225fcb4682e66ac4ffa00c1af475532b95971a6aa9aa7af29871b189", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.6.0", "os": "win", "version": "1.7.0", "date": "2026-05-14T09:47:39.000Z", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "a34e8a06807e38900ca7405986c9f3aed0f367b7cbae027b4b8c013154b2cae1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.0", "date": "2026-05-22T08:34:06.000Z", "commit": "98febcffc151698b961f2016926855bb407d6e6a", "fileid": "74e1036499f6ae8f51ae3143eba2a1d6ddedea16b66491be611d90d50a5232c2", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25853153074" } ] }