{ "_id": "6a11614cacfb0bcc41cedc5f", "Package": "ceas", "Title": "Cellular Energetics Analysis Software", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Rachel\", \"House\", email = \"rachel.house@vai.org\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-2176-0431\")),\nperson(\"James P.\", \"Eapen\", email = \"james.eapen@vai.org\", role = c(\"aut\"), comment = c(ORCID = \"0000-0001-6016-3598\")),\nperson(\"Hui\", \"Shen\", email = \"hui.shen@vai.org\", role = c(\"fnd\"), comment = c(ORCID = \"0000-0001-9767-4084\")),\nperson(\"Carrie R.\", \"Graveel\", email = \"carrie.graveel@vai.org\", role = c(\"fnd\"), comment = c(ORCID = \"0000-0001-7251-5642\")),\nperson(\"Matthew R.\", \"Steensma\", email = \"matthew.steensma@vai.org\", role = c(\"fnd\"), comment = c(ORCID = \"0000-0002-9003-6730\")),\nperson(\"Van Andel Institute\", role = c(\"cph\")))", "Description": "Measuring cellular energetics is essential to\nunderstanding a matrix’s (e.g. cell, tissue or biofluid)\nmetabolic state. The Agilent Seahorse machine is a common\nmethod to measure real-time cellular energetics, but existing\nanalysis tools are highly manual or lack functionality. The\nCellular Energetics Analysis Software (ceas) R package fills\nthis analytical gap by providing modular and automated Seahorse\ndata analysis and visualization using the methods described by\nMookerjee et al. (2017) .", "URL": "https://jamespeapen.github.io/ceas/,\nhttps://github.com/jamespeapen/ceas/", "BugReports": "https://github.com/jamespeapen/ceas/issues/", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make", "Repository": "https://jamespeapen.r-universe.dev", "Date/Publication": "2024-12-20 20:39:04 UTC", "RemoteUrl": "https://github.com/jamespeapen/ceas", "RemoteRef": "HEAD", "RemoteSha": "f638894b1d9cb792d1133aeb8b889a31981460f6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 08:08:23 UTC", "User": "root" }, "Author": "Rachel House [aut, cre] (ORCID:\n),\nJames P. Eapen [aut] (ORCID: ),\nHui Shen [fnd] (ORCID: ),\nCarrie R. Graveel [fnd] (ORCID:\n),\nMatthew R. Steensma [fnd] (ORCID:\n),\nVan Andel Institute [cph]", "Maintainer": "Rachel House ", "MD5sum": "f96cad44874308e3649b6b7d7fb4aa9a", "_user": "jamespeapen", "_type": "src", "_file": "ceas_1.3.0.tar.gz", "_fileid": "8a17fa035abd35e498893a60aba5f6bd9f119afde668c56d52745a19b68dade5", "_filesize": 3583604, "_sha256": "8a17fa035abd35e498893a60aba5f6bd9f119afde668c56d52745a19b68dade5", "_created": "2026-05-23T08:08:23.000Z", "_published": "2026-05-23T08:11:56.201Z", "_distro": "noble", "_jobs": [ { "job": 77508345044, "time": 174, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175542898" }, { "job": 77508345045, "time": 164, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175542170" }, { "job": 77508345037, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175538831" }, { "job": 77508345034, "time": 142, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175537830" }, { "job": 77508170033, "time": 202, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175526683" }, { "job": 77508345030, "time": 111, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175537169" }, { "job": 77508345061, "time": 120, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175538445" }, { "job": 77508345059, "time": 132, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175539105" }, { "job": 77508345053, "time": 130, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175538971" } ], "_buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jamespeapen/ceas", "_commit": { "id": "f638894b1d9cb792d1133aeb8b889a31981460f6", "author": "James Eapen ", "committer": "James Eapen ", "message": "docs(pkgdown): updates to wording\n\n- input format\n- alternative assay types\n- getting rep list from dir\n", "time": 1734727144 }, "_maintainer": { "name": "Rachel House", "email": "rachel.house@vai.org", "orcid": "0000-0003-2176-0431" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "readxl", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "jamespeapen", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "jamespeapen", "count": 191, "uuid": 39574560 }, { "user": "raehouse", "count": 5, "uuid": 52250729 } ], "_userbio": { "uuid": 39574560, "type": "user", "name": "James Eapen", "description": "PhD student in computational biology" }, "_downloads": { "count": 215, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ceas" }, "_devurl": "https://github.com/jamespeapen/ceas", "_pkgdown": "https://jamespeapen.github.io/ceas/", "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/ceas.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/jamespeapen/ceas", "_realowner": "jamespeapen", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2024-05-07" }, { "version": "1.3.0", "date": "2024-12-21" } ], "_exports": [ "atp_plot", "bioscope_plot", "energetics_lme_summary", "energetics_ols_summary", "fit_lme", "get_energetics", "get_energetics_summary", "get_rate_summary", "make_bioscope_plot", "normalize", "partition_data", "rate_plot", "rates_lme_summary", "read_data" ], "_help": [ { "page": "atp_plot", "title": "ATP Plot", "topics": [ "atp_plot" ] }, { "page": "bioscope_plot", "title": "Bioenergetic Scope Plot", "topics": [ "bioscope_plot" ] }, { "page": "energetics_lme_summary", "title": "Get mean and confidence intervals from energetics mixed-effects models", "topics": [ "energetics_lme_summary" ] }, { "page": "energetics_ols_summary", "title": "Get ordinary least squares mean and confidence intervals from energetics", "topics": [ "energetics_ols_summary" ] }, { "page": "get_energetics", "title": "Calculate ATP Production from OXPHOS and Glycolysis", "topics": [ "get_energetics" ] }, { "page": "get_energetics_summary", "title": "Calculate ATP Production Mean and Standard Deviation", "topics": [ "get_energetics_summary" ] }, { "page": "get_rate_summary", "title": "Rates summary", "topics": [ "get_rate_summary" ] }, { "page": "make_bioscope_plot", "title": "Bioenergetic Scope Plot Shortcut", "topics": [ "make_bioscope_plot" ] }, { "page": "normalize", "title": "Normalize Seahorse data", "topics": [ "normalize" ] }, { "page": "partition_data", "title": "Organize Seahorse Data", "topics": [ "partition_data" ] }, { "page": "rate_plot", "title": "Rate plot", "topics": [ "rate_plot" ] }, { "page": "read_data", "title": "Read Seahorse Wave Excel File", "topics": [ "read_data" ] } ], "_pkglogo": "https://github.com/jamespeapen/ceas/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/jamespeapen/ceas/raw/HEAD/README.md", "_rundeps": [ "boot", "cellranger", "cli", "cpp11", "crayon", "data.table", "farver", "ggplot2", "glue", "gtable", "hms", "isoband", "labeling", "lattice", "lifecycle", "lme4", "magrittr", "MASS", "Matrix", "minqa", "nlme", "nloptr", "pillar", "pkgconfig", "prettyunits", "progress", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "readxl", "reformulas", "rematch", "rlang", "S7", "scales", "tibble", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "atp_calculation.Rmd", "filename": "atp_calculation.html", "title": "ATP calculation", "engine": "knitr::rmarkdown", "headings": [], "created": "2023-12-21 16:17:19", "modified": "2023-12-21 16:17:19", "commits": 1 }, { "source": "ceas.Rmd", "filename": "ceas.html", "title": "Getting started with CEAS", "engine": "knitr::rmarkdown", "headings": [ "Setup", "Importing Seahorse rates data", "Normalization", "Calculating energetics", "Partitioning data", "Alternative data formats", "Mito + Glyco (our default)", "Data in the form of @mookerjee2017", "Just Mito", "Respiratory control ratio (RCR) and glycolytic capacity (GC) assay", "", "Plotting", "Bioenergetic scope plot", "Replicates combined", "Replicates as random effects", "Replicates separated", "Rate plots", "Oxygen consumption rate (OCR)", "Extracellular Acidification Rate (ECAR)", "ATP plots", "Basal glycolysis", "Basal respiration", "Maximal glycolysis", "Maximal respiration", "Customizing plots", "Colors", "Labels", "Change axis labels", "Change label size", "Editing functions", "References" ], "created": "2023-12-21 16:17:19", "modified": "2024-12-20 20:39:04", "commits": 9 } ], "_score": 4.301029995663981, "_indexed": true, "_nocasepkg": "ceas", "_universes": [ "jamespeapen" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-05-23T08:10:46.000Z", "distro": "noble", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "cd0a734804ef1eff1c4a8961a36e8fb4bc365a61621336c00938dbb0c6248c55", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-05-23T08:10:43.000Z", "distro": "noble", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "884b32892f1f817280d8eb1becd4e9184fec69105d92b105d9f53913f215536c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.5.3", "os": "mac", "version": "1.3.0", "date": "2026-05-23T08:10:28.000Z", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "26f266fac917ea841f8659291eed309ac14108c4f28799fcfc7526c9c2f3e0c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.6.0", "os": "mac", "version": "1.3.0", "date": "2026-05-23T08:10:14.000Z", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "a26b5926aa511945346a4918fcbce7a3640a2427067af2436c3eeee860314cb8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-05-23T08:10:34.000Z", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "d63ba530af7f2af5e523df85b83f769c2babcc244d6cda505a0c977f19f78add", "status": "success", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.7.0", "os": "win", "version": "1.3.0", "date": "2026-05-23T08:09:57.000Z", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "c9bd57a847588cb3570f1a992ebe9c520c8b83574a2dfb876450d198b4f5a715", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.5.3", "os": "win", "version": "1.3.0", "date": "2026-05-23T08:09:54.000Z", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "69586ee9cc37a34da958a0e65d61345d3021db3fdeb63c9ee70a34bce2e3744d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" }, { "r": "4.6.0", "os": "win", "version": "1.3.0", "date": "2026-05-23T08:09:59.000Z", "commit": "f638894b1d9cb792d1133aeb8b889a31981460f6", "fileid": "3472a1185e3c08e9ef30f3306670eb6a18a9a96535915da37f9f89f0eac71f65", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jamespeapen/actions/runs/26327658524" } ] }