{ "_id": "6a1f0d79b401979e7341d061", "Package": "DamageDetective", "Type": "Package", "Title": "Detecting Damaged Cells in Single-Cell RNA Sequencing Data", "Version": "2.0.15", "Authors@R": "person(\"Alicen\", \"Henning\", email = \"alicen.jhb@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0009-0004-0535-1624\"))", "Description": "Detects and filters damaged cells in single-cell RNA\nsequencing (scRNA-seq) data using a novel approach inspired by\n'DoubletFinder'. Damage is assessed by measuring how much each\ncell deviates from an artificially damaged version of itself,\nsimulated through the probabilistic loss of cytoplasmic RNA.\nThe method outputs a damage score ranging from 0 (viable,\nintact cell) to 1 (broken, non-viable cell), providing an\nintuitive scale for filtering that is standardised across cell\ntypes, sample origin, and experimental design.", "License": "AGPL (>= 3)", "Encoding": "UTF-8", "Language": "en-US", "LazyData": "false", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "URL": "https://alicenjoyhenning.github.io/DamageDetective/,\nhttps://github.com/alicenjoyhenning/DamageDetective", "BugReports": "https://github.com/alicenjoyhenning/DamageDetective/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://alicenjoyhenning.r-universe.dev", "Date/Publication": "2025-10-19 04:19:18 UTC", "RemoteUrl": "https://github.com/alicenjoyhenning/damagedetective", "RemoteRef": "HEAD", "RemoteSha": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-17 09:06:12 UTC", "User": "root" }, "Author": "Alicen Henning [aut, cre, cph] (ORCID:\n)", "Maintainer": "Alicen Henning ", "MD5sum": "0e475e8a771ea0b7876969de04272273", "_user": "alicenjoyhenning", "_type": "src", "_file": "DamageDetective_2.0.15.tar.gz", "_fileid": "e64e18a18861591cc6f980c75c083e86debdbfaa71c9fbb73dbae31f56295ff9", "_filesize": 1374722, "_sha256": "e64e18a18861591cc6f980c75c083e86debdbfaa71c9fbb73dbae31f56295ff9", "_created": "2026-05-17T09:06:12.000Z", "_published": "2026-06-02T17:06:01.313Z", "_distro": "noble", "_jobs": [ { "job": 79127520881, "time": 274, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7041106321" }, { "job": 79127520482, "time": 294, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7041108566" }, { "job": 79127520720, "time": 257, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7041104189" }, { "job": 79127521295, "time": 284, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7041107510" }, { "job": 79127521128, "time": 287, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7041105243" }, { "job": 79127520652, "time": 605, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7041135998" }, { "job": 79127520605, "time": 312, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7041106624" }, { "job": 79127520465, "time": 609, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7041139714" }, { "job": 79127520095, "time": 304, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7041075512" }, { "job": 79127519537, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7364604788" }, { "job": 79127520530, "time": 251, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7041103418" }, { "job": 79127521028, "time": 263, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7041105002" }, { "job": 79127520664, "time": 249, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7041103420" } ], "_buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/alicenjoyhenning/damagedetective", "_commit": { "id": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "author": "Alicen Henning <129797527+AlicenJoyHenning@users.noreply.github.com>", "committer": "Alicen Henning <129797527+AlicenJoyHenning@users.noreply.github.com>", "message": "Update R-CMD-check.yaml\n\nNothing changed on my side but:\n\nError: ! error in pak subprocess Caused by error in select_next_task(state): ! Cannot select new package installation task.\n\nAvoid using pak to avoid the pkgdepends bug entirely.\n", "time": 1760847558 }, "_maintainer": { "name": "Alicen Henning", "email": "alicen.jhb@gmail.com", "login": "alicenjoyhenning", "linkedin": "in/alicen-joy-henning-b41b09223", "description": "Postgrad in Bioinformatics and Computational Biology at Stellenbosch University", "uuid": 129797527 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "cowplot", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "e1071", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "RcppHNSW", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "alicenjoyhenning", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-20", "n": 1 }, { "week": "2025-21", "n": 2 }, { "week": "2025-27", "n": 1 }, { "week": "2025-28", "n": 6 }, { "week": "2025-29", "n": 3 }, { "week": "2025-35", "n": 2 }, { "week": "2025-36", "n": 12 }, { "week": "2025-37", "n": 2 }, { "week": "2025-39", "n": 8 }, { "week": "2025-42", "n": 1 } ], "_tags": [], "_stars": 3, "_contributors": [ { "user": "alicenjoyhenning", "count": 165, "uuid": 129797527 } ], "_userbio": { "uuid": 129797527, "type": "user", "name": "Alicen Henning", "description": "Postgrad in Bioinformatics and Computational Biology at Stellenbosch University" }, "_downloads": { "count": 182, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/DamageDetective" }, "_devurl": "https://github.com/alicenjoyhenning/damagedetective", "_pkgdown": "https://alicenjoyhenning.github.io/DamageDetective/", "_searchresults": 9, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DamageDetective.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/alicenjoyhenning/damagedetective", "_realowner": "alicenjoyhenning", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2025-04-03" } ], "_exports": [ "detect_damage", "select_penalty", "simulate_counts" ], "_datasets": [ { "name": "filtered_output", "title": "Filtered Output", "object": "filtered_output", "file": "filtered_output.rda", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "penalty_plot", "title": "Penalty Plot", "object": "penalty_plot", "file": "penalty_plot.rda", "class": [ "patchwork", "gg", "ggplot" ], "fields": [], "table": false, "tojson": false }, { "name": "selected_penalty", "title": "Selected Penalty", "object": "selected_penalty", "file": "selected_penalty.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "test_counts", "title": "Test Counts", "object": "test_counts", "file": "test_counts.rda", "class": [ "dgCMatrix" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "detect_damage", "title": "detect_damage", "topics": [ "detect_damage" ] }, { "page": "filtered_output", "title": "Filtered Output", "topics": [ "filtered_output" ] }, { "page": "penalty_plot", "title": "Penalty Plot", "topics": [ "penalty_plot" ] }, { "page": "select_penalty", "title": "select_penalty", "topics": [ "select_penalty" ] }, { "page": "selected_penalty", "title": "Selected Penalty", "topics": [ "selected_penalty" ] }, { "page": "simulate_counts", "title": "simulate_counts", "topics": [ "simulate_counts" ] }, { "page": "test_counts", "title": "Test Counts", "topics": [ "test_counts" ] } ], "_pkglogo": "https://github.com/alicenjoyhenning/damagedetective/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/alicenjoyhenning/damagedetective/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "base64enc", "BH", "bitops", "boot", "broom", "bslib", "cachem", "car", "carData", "caTools", "class", "cli", "cluster", "codetools", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "deldir", "Deriv", "digest", "doBy", "dotCall64", "dplyr", "dqrng", "e1071", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "future", "future.apply", "generics", "ggplot2", "ggpubr", "ggrepel", "ggridges", "ggsci", "ggsignif", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lme4", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "miniUI", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pbkrtest", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "polynom", "progressr", "promises", "proxy", "purrr", "quantreg", "R6", "RANN", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppTOML", "Rdpack", "reformulas", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "rstatix", "Rtsne", "S7", "sass", "scales", "scattermore", "sctransform", "Seurat", "SeuratObject", "shiny", "sitmo", "sourcetools", "sp", "spam", "SparseM", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "survival", "sys", "tensor", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "urca", "utf8", "uwot", "vctrs", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "detection-vignette.Rmd", "filename": "detection-vignette.html", "title": "DamageDetective Overview", "engine": "knitr::rmarkdown", "headings": [ "Package description", "Prerequisites", "Libraries", "Input data formatting", "Parameter selection", "select_penalty", "filter_threshold", "Running damaged cell detection", "Session Information" ], "created": "2025-03-28 17:42:06", "modified": "2025-04-29 11:56:42", "commits": 24 } ], "_score": 5.176091259055681, "_indexed": true, "_nocasepkg": "damagedetective", "_universes": [ "alicenjoyhenning" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.15", "date": "2026-05-17T09:09:25.000Z", "distro": "noble", "arch": "aarch64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "0d23e910b24f00565c9c6d6aa36a6a23a05232dc517fd3a61cbc8110ee27b6e2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.7.0", "os": "linux", "version": "2.0.15", "date": "2026-05-17T09:09:38.000Z", "distro": "noble", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "885614347133ddca319bb99233a6e4d3d28b5c298c9deea28e82ece71f4286f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.6.0", "os": "linux", "version": "2.0.15", "date": "2026-05-17T09:09:18.000Z", "distro": "noble", "arch": "aarch64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "107919344932571882131c8108c34cee5fbf31aa401dd33b23c9cd231edca041", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.6.0", "os": "linux", "version": "2.0.15", "date": "2026-05-17T09:09:34.000Z", "distro": "noble", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "07fcd48c8d117575fb1bbbe3a7c269baa50b8a09861db66de62cf15c44c3310f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.5.3", "os": "mac", "version": "2.0.15", "date": "2026-05-17T09:09:21.000Z", "arch": "aarch64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "23efd60c7e968ac448419ba04568bf92266aa1ce7b19829e4e0b72002e8474d7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.5.3", "os": "mac", "version": "2.0.15", "date": "2026-05-17T09:11:13.000Z", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "0d53830e9a5fdf2ad83b66796d9dcf3010e874fef0accab36800966336bfb04b", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.6.0", "os": "mac", "version": "2.0.15", "date": "2026-05-17T09:09:16.000Z", "arch": "aarch64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "a5030513789d0079d69b327ab34875e5a1e8149bd4e8d19305948cf2599f667c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.6.0", "os": "mac", "version": "2.0.15", "date": "2026-05-17T09:11:28.000Z", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "7a1e2107ac5af0aced17227fece2fd93d21112b845183d6e7f3ca59ad0f10725", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.7.0", "os": "win", "version": "2.0.15", "date": "2026-05-17T09:08:38.000Z", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "f2757abccfb966aaf4832e60f21bf1f07ba6accdf6f1f9efc46e5d66caa94266", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.5.3", "os": "win", "version": "2.0.15", "date": "2026-05-17T09:08:42.000Z", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "e48af671a4843c9aed2074953613446d1b51b9d7a11df15db20f51ee73172471", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.6.0", "os": "win", "version": "2.0.15", "date": "2026-05-17T09:08:11.000Z", "arch": "x86_64", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "1ff8ca1284d2f966a6b8d0030057680bf749c9970bb1edc33d39f74396be0bd0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" }, { "r": "4.6.0", "os": "wasm", "version": "2.0.15", "date": "2026-06-02T17:05:31.000Z", "arch": "emscripten", "commit": "3d21be2175fcb29e9f68f301640e8386bf8a1c5c", "fileid": "b1cf8888fab5c9090bc04f93acf4d51f799a5bbbeb3ad49b4022f69f759d3b20", "status": "success", "buildurl": "https://github.com/r-universe/alicenjoyhenning/actions/runs/25986551905" } ] }