{ "_id": "6a586f41ff0138dec5d735a1", "Package": "staRgate", "Title": "Automated gating pipeline for flow cytometry analysis to\ncharacterize the lineage, differentiation, and functional\nstates of T-cells", "Version": "1.1.0", "Authors@R": "c(\nperson(\"Jasme\", \"Lee\", email = \"leej22@mskcc.org\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0006-4492-4872\")),\nperson(\"Matthew\", \"Adamow\", role = c(\"aut\")),\nperson(\"Colleen\", \"Maher\", role = c(\"aut\")),\nperson(\"Xiyu\", \"Peng\", role = c(\"aut\")),\nperson(\"Phillip\", \"Wong\", role = c(\"aut\")),\nperson(\"Fiona\", \"Ehrich\", role = c(\"aut\")),\nperson(\"Michael\", \"Postow\", middle = \"A\", role = c(\"aut\")),\nperson(\"Margaret\", \"Callahan\", middle = \"K\", role = c(\"aut\")),\nperson(\"Ronglai\", \"Shen\", role = c(\"aut\")),\nperson(\"Katherine\", \"Panageas\", middle = \"S\", role = c(\"aut\")),\nperson(\"V foundation\", role = \"fnd\"),\nperson(\"MSK-MIND\", role = \"fnd\"),\nperson(\"NIH R01CA276286\", role = \"fnd\"),\nperson(\"NIH P30CA008748\", role = \"fnd\")\n)", "Description": "An R-based automated gating pipeline for flow cytometry\ndata designed to mimic the manual gating strategy of defining\nflow biomarker positive populations relative to a unimodal\nbackground population to include cells with varying intensities\nof marker expression. The pipeline’s main feature is a flexible\ndensity-based gating strategy capable of capturing varying\nscenarios based on marker expression patterns to analyze a\n29-marker flow panel that characterizes T-cell lineage,\ndifferentiation, and functional states.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "biocViews": "FlowCytometry, Preprocessing, ImmunoOncology", "VignetteBuilder": "knitr", "BugReports": "https://github.com/leejasme/staRgate/issues", "URL": "https://bioconductor.org/packages/staRgate,\nhttps://leejasme.github.io/staRgate", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libicu-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:06:11 UTC", "RemoteUrl": "https://github.com/bioc/staRgate", "RemoteRef": "HEAD", "RemoteSha": "64cb14695c16827a15d097c41d2dc26a5748626a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-16 05:19:21 UTC", "User": "root" }, "Author": "Jasme Lee [aut, cre] (ORCID: ),\nMatthew Adamow [aut],\nColleen Maher [aut],\nXiyu Peng [aut],\nPhillip Wong [aut],\nFiona Ehrich [aut],\nMichael A Postow [aut],\nMargaret K Callahan [aut],\nRonglai Shen [aut],\nKatherine S Panageas [aut],\nV foundation [fnd],\nMSK-MIND [fnd],\nNIH R01CA276286 [fnd],\nNIH P30CA008748 [fnd]", "Maintainer": "Jasme Lee ", "_user": "bioc", "_type": "src", "_file": "staRgate_1.1.0.tar.gz", "_fileid": "https://r2.ropensci.org/92f614e131e3532d791edc2e1baf6df11e22db0195bb1c87c51fcde3629622ff", "_filesize": 5631307, "_sha256": "92f614e131e3532d791edc2e1baf6df11e22db0195bb1c87c51fcde3629622ff", "_expires": "2026-10-24T05:42:22.000Z", "_created": "2026-07-16T05:19:21.000Z", "_published": "2026-07-16T05:42:24.751Z", "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672", "_status": "success", "_upstream": "https://github.com/bioc/staRgate", "_commit": { "id": "64cb14695c16827a15d097c41d2dc26a5748626a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381571 }, "_maintainer": { "name": "Jasme Lee", "email": "leej22@mskcc.org", "orcid": "0009-0006-4492-4872" }, "_distro": "resolute", "_jobs": [ { "job": 87541687240, "time": 172, "config": "bioc-checks", "r": "4.6.1", "check": "WARNING", "artifact": "8365731476" }, { "job": 87541687248, "time": 241, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8365750263" }, { "job": 87541687234, "time": 221, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8365744519" }, { "job": 87541687247, "time": 103, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8366035398" }, { "job": 87541687241, "time": 140, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8366045998" }, { "job": 87541160025, "time": 230, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8365684135" }, { "job": 87541687237, "time": 153, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8365726786" }, { "job": 87541687244, "time": 108, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8365714295" }, { "job": 87541687226, "time": 137, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8365722912" }, { "job": 87541687261, "time": 124, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8365718985" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "janitor", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "flowCore", "role": "Imports" }, { "package": "flowWorkspace", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "flowAI", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "gt", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "openCyto", "role": "Suggests" }, { "package": "ggcyto", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "data.table", "role": "Suggests" }, { "package": "here", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-40", "n": 1 }, { "week": "2025-41", "n": 1 }, { "week": "2025-42", "n": 2 }, { "week": "2025-46", "n": 2 }, { "week": "2025-47", "n": 3 }, { "week": "2026-04", "n": 4 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 6 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.1.0", "bioc": "3.24" }, { "branch": "release", "version": "1.0.0", "bioc": "3.23" } ], "_topics": [ "flowcytometry", "preprocessing", "immunooncology" ], "_stars": 3, "_contributors": [ { "user": "leejasme", "count": 126, "uuid": 61248192 }, { "user": "karissawhiting", "count": 2, "uuid": 10888683 }, { "user": "hkalvin", "count": 1, "uuid": 71410068 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 447, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 194, "source": "https://www.bioconductor.org/packages/stats/bioc/staRgate" }, "_devurl": "https://github.com/leejasme/stargate", "_pkgdown": "https://leejasme.github.io/staRgate", "_searchresults": 2, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/staRgate.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/leejasme/stargate", "_realowner": "bioc", "_cranurl": false, "_exports": [ "getBiexpTransformGS", "getCompGS", "getDensityGates", "getGatedDat", "getPerc" ], "_help": [ { "page": "getBiexpTransformGS", "title": "Applies Biexpeonential Transformation using specifications in csv file provided at 'path_biexp_params'", "topics": [ "getBiexpTransformGS" ] }, { "page": "getCompGS", "title": "Applies Compensation using specifications in csv file provided at 'path_comp_mat'", "topics": [ "getCompGS" ] }, { "page": "getDensityGates", "title": "Density gating of intensity values in 'marker' for each unique subset of 'subset_col'", "topics": [ "getDensityGates" ] }, { "page": "getGatedDat", "title": "Attach indicator columns to 'intens_dat' based on gates provided in 'cutoffs'", "topics": [ "getGatedDat" ] }, { "page": "getPerc", "title": "Calculate the percentage of positive cells for specific subpopulations", "topics": [ "getPerc" ] } ], "_pkglogo": "https://github.com/bioc/staRgate/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/staRgate/raw/HEAD/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "biocmake", "cli", "cpp11", "cytolib", "data.table", "DelayedArray", "dir.expiry", "dplyr", "farver", "filelock", "flowCore", "flowWorkspace", "generics", "ggplot2", "glue", "graph", "gtable", "hms", "IRanges", "isoband", "janitor", "labeling", "lattice", "lifecycle", "lubridate", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "ncdfFlow", "pillar", "pkgconfig", "purrr", "R6", "RBGL", "RColorBrewer", "Rcpp", "Rgraphviz", "Rhdf5lib", "rlang", "RProtoBufLib", "S4Arrays", "S4Vectors", "S7", "scales", "snakecase", "SparseArray", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timechange", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector" ], "_vignettes": [ { "source": "vignette_run_pipeline.Rmd", "filename": "vignette_run_pipeline.html", "title": "Tutorial: Running the pipeline", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Input files and function parameters", "Example", "Import FCS", "Compensation", "Transformation", "Pre-gating", "Extract intensity matrix", "Gating on T-cell subsets", "Pseudo-negative control", "Empirical gating", "Visualizing the gates", "LAG3 for all CD3+", "LAG3 by CD4 and CD8 subsets", "CCR7 for all CD3+", "CCR7 by CD4 and CD8 subsets", "CD45RA for all CD3+", "CD45RA by CD4 and CD8 subsets", "CD127 for all CD3+", "CD127 by CD4 and CD8 subsets", "CD28 for all CD3+", "CD28 by CD4 and CD8 subsets", "", "Getting percentage data", "Optional: Adding density gates back to GatingSet", "Session info", "References" ], "created": "2023-06-01 18:37:15", "modified": "2025-11-19 19:29:43", "commits": 38 } ], "_score": 5.431363764158988, "_indexed": true, "_nocasepkg": "stargate", "_universes": [ "bioc", "leejasme" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.0", "date": "2026-07-16T05:23:15.000Z", "distro": "resolute", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/652dc878ce9944bce93358391501dfffa7d54a9a3da1d5af6419c79a10cc7d94", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.6.1", "os": "linux", "version": "1.1.0", "date": "2026-07-16T05:22:57.000Z", "distro": "resolute", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/e1b875bec4daf6893c3cd54ad69c0835373817b0b1304477ba35dca3ce62004b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.5.3", "os": "mac", "version": "1.1.0", "date": "2026-07-16T05:41:03.000Z", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/1b3431492f6d9401a8dee2080ac0a9f077373c0464c1a8de364934d41036d57a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.6.1", "os": "mac", "version": "1.1.0", "date": "2026-07-16T05:41:34.000Z", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/b0d517376ad4f0805567e037669865c2b23a5a0d7b0098c3252bbeafb2bebce7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.6.0", "os": "wasm", "version": "1.1.0", "date": "2026-07-16T05:22:09.000Z", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/416413b1ac712b57b4848eb63787867a88f42fd2807be0b7400eea0946577a16", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.7.0", "os": "win", "version": "1.1.0", "date": "2026-07-16T05:20:51.000Z", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/cd4883514dee0be510055b7a25eff5634e198300cb4c22216cf401b37b7407fe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.5.3", "os": "win", "version": "1.1.0", "date": "2026-07-16T05:21:26.000Z", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/1f9ae60294581caaceeb52824a7ff4dc7ad539962bb375ab21b39c69bc22d66f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" }, { "r": "4.6.1", "os": "win", "version": "1.1.0", "date": "2026-07-16T05:21:14.000Z", "commit": "64cb14695c16827a15d097c41d2dc26a5748626a", "fileid": "https://r2.ropensci.org/e14e0e6b166070a9b8b471f59daf3bc638c7f1022844dac6bce4a4b94cabd39c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29473418672" } ] }