{ "_id": "6aca8cc0fe5cc25786e8b49d", "Package": "Polytect", "Title": "An R package for digital data clustering", "Version": "1.5.0", "Authors@R": "person(\"Yao\", \"Chen\", , \"emmachentar@live.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-8172-3996\"))", "Description": "Polytect is an advanced computational tool designed for\nthe analysis of multi-color digital PCR data. It provides\nautomatic clustering and labeling of partitions into distinct\ngroups based on clusters first identified by the flowPeaks\nalgorithm. Polytect is particularly useful for researchers in\nmolecular biology and bioinformatics, enabling them to gain\ndeeper insights into their experimental results through precise\npartition classification and data visualization.", "biocViews": "ddPCR, Clustering, MultiChannel, Classification", "License": "Artistic-2.0", "URL": "https://github.com/emmachenlingo/Polytect", "BugReports": "https://github.com/emmachenlingo/Polytect/issues", "Encoding": "UTF-8", "LazyData": "false", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev libgdal-dev gdal-bin libgeos-dev\nlibglu1-mesa-dev libgmp3-dev make libgsl0-dev libharfbuzz-dev\njags libicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev\nlibwebp-dev libxml2-dev libmpfr-dev libopenmpi-dev libssl-dev\nlibproj-dev libx11-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:08 UTC", "RemoteUrl": "https://github.com/bioc/Polytect", "RemoteRef": "HEAD", "RemoteSha": "48dacdd5c28012320783eaacc5393c42e200652a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-10 17:42:17 UTC", "User": "root" }, "Author": "Yao Chen [aut, cre] (ORCID: )", "Maintainer": "Yao Chen ", "_user": "bioc", "_type": "src", "_file": "Polytect_1.5.0.tar.gz", "_fileid": "https://r2.ropensci.org/a3f78442df62cc3bc52fba60fcbe01c0ba07620dc3932b269336f183c1e04967", "_filesize": 2611329, "_sha256": "a3f78442df62cc3bc52fba60fcbe01c0ba07620dc3932b269336f183c1e04967", "_expires": "2027-01-18T19:06:37.000Z", "_created": "2026-10-10T17:42:17.000Z", "_published": "2026-10-10T19:06:39.913Z", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 3 }, "_upstream": "https://github.com/bioc/Polytect", "_commit": { "id": "48dacdd5c28012320783eaacc5393c42e200652a", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381448 }, "_maintainer": { "name": "Yao Chen", "email": "emmachentar@live.com", "login": "emmachenlingo", "description": "", "uuid": 21023485, "orcid": "0000-0001-8172-3996" }, "_distro": "resolute", "_jobs": [ { "job": 114273669011, "time": 194, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11677249309" }, { "job": 114273669093, "time": 256, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11677239517" }, { "job": 114273669037, "time": 296, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11677830805" }, { "job": 114273669028, "time": 180, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "11679695122" }, { "job": 114273668983, "time": 172, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "11679463971" }, { "job": 114272635559, "time": 311, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11676954573" }, { "job": 114273669108, "time": 157, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11677004879" }, { "job": 114273669053, "time": 196, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "11677297016" }, { "job": 114273669060, "time": 179, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "11677044916" }, { "job": 114273669061, "time": 180, "config": "windows-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "11677925388" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "mvtnorm", "role": "Imports" }, { "package": "sn", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "flowPeaks", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "tidyverse", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "mlrMBO", "role": "Imports" }, { "package": "DiceKriging", "role": "Imports" }, { "package": "smoof", "role": "Imports" }, { "package": "ParamHelpers", "role": "Imports" }, { "package": "lhs", "role": "Imports" }, { "package": "rgenoud", "role": "Imports" }, { "package": "BiocManager", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ddPCRclust", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.5.0", "bioc": "3.24", "repository": "bioc" }, { "branch": "release", "version": "1.4.0", "bioc": "3.23", "repository": "bioc" } ], "_topics": [ "ddpcr", "clustering", "multichannel", "classification" ], "_stars": 1, "_contributors": [ { "user": "emmachenlingo", "count": 44, "uuid": 21023485 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 476, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 214, "source": "https://www.bioconductor.org/packages/stats/bioc/Polytect" }, "_devurl": "https://github.com/emmachenlingo/polytect", "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/Polytect.html", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/emmachenlingo/polytect", "_realowner": "bioc", "_cranurl": false, "_exports": [ "conc_cal", "polytect_clust", "polytect_merge", "polytect_plot", "polytect_summary", "sil_plot" ], "_datasets": [ { "name": "BPV", "title": "BPV data", "object": "BPV", "file": "BPV.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2", "channel3" ], "rows": 25461, "table": true, "tojson": true }, { "name": "CA", "title": "CA data", "object": "CA", "file": "CA.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2" ], "rows": 23863, "table": true, "tojson": true }, { "name": "CNV5plex", "title": "CNV 5-plex data", "object": "CNV5plex", "file": "CNV5plex.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2", "channel3", "channel4", "channel5" ], "rows": 24827, "table": true, "tojson": true }, { "name": "CNV6plex", "title": "CNV 6-plex data", "object": "CNV6plex", "file": "CNV6plex.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2", "channel3", "channel4", "channel5", "channel6" ], "rows": 24483, "table": true, "tojson": true }, { "name": "HIV", "title": "HIV data", "object": "HIV", "file": "HIV.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2", "channel3", "channel4" ], "rows": 16946, "table": true, "tojson": true }, { "name": "HR", "title": "HR data", "object": "HR", "file": "HR.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2" ], "rows": 18233, "table": true, "tojson": true }, { "name": "LR", "title": "LR data", "object": "LR", "file": "LR.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2" ], "rows": 22723, "table": true, "tojson": true }, { "name": "MM", "title": "MM data", "object": "MM", "file": "MM.rda", "class": [ "data.frame" ], "fields": [ "channel1", "channel2" ], "rows": 14203, "table": true, "tojson": true } ], "_help": [ { "page": "BPV", "title": "BPV data", "topics": [ "BPV" ] }, { "page": "CA", "title": "CA data", "topics": [ "CA" ] }, { "page": "CNV5plex", "title": "CNV 5-plex data", "topics": [ "CNV5plex" ] }, { "page": "CNV6plex", "title": "CNV 6-plex data", "topics": [ "CNV6plex" ] }, { "page": "conc_cal", "title": "concentration calculation function", "topics": [ "conc_cal" ] }, { "page": "HIV", "title": "HIV data", "topics": [ "HIV" ] }, { "page": "HR", "title": "HR data", "topics": [ "HR" ] }, { "page": "LR", "title": "LR data", "topics": [ "LR" ] }, { "page": "MM", "title": "MM data", "topics": [ "MM" ] }, { "page": "polytect_clust", "title": "Main function for clustering", "topics": [ "polytect_clust" ] }, { "page": "polytect_merge", "title": "Function for merging", "topics": [ "polytect_merge" ] }, { "page": "polytect_plot", "title": "Plotting function for clustering results", "topics": [ "polytect_plot" ] }, { "page": "polytect_summary", "title": "Summary function", "topics": [ "polytect_summary" ] }, { "page": "sil_plot", "title": "Plotting function for silhouette coefficients", "topics": [ "sil_plot" ] } ], "_readme": "https://github.com/bioc/Polytect/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "base64enc", "BBmisc", "BiocManager", "bit", "bit64", "blob", "broom", "bslib", "cachem", "callr", "cellranger", "checkmate", "cli", "clipr", "conflicted", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DiceKriging", "digest", "dplyr", "dtplyr", "evaluate", "farver", "fastmap", "fastmatch", "flowPeaks", "fontawesome", "forcats", "fs", "gargle", "generics", "ggplot2", "glue", "googledrive", "googlesheets4", "gtable", "haven", "highr", "hms", "htmltools", "httr", "ids", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lhs", "lifecycle", "lubridate", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "mime", "mlr", "mlrMBO", "mnormt", "modelr", "mvtnorm", "numDeriv", "openssl", "otel", "parallelMap", "ParamHelpers", "pillar", "pkgconfig", "prettyunits", "processx", "progress", "ps", "purrr", "quantreg", "R6", "ragg", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "readr", "readxl", "rematch", "rematch2", "reprex", "rgenoud", "rlang", "rmarkdown", "rstudioapi", "rvest", "S7", "sass", "scales", "selectr", "smoof", "sn", "SparseM", "stringi", "stringr", "survival", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tidyverse", "timechange", "tinytex", "tzdb", "utf8", "uuid", "vctrs", "viridisLite", "vroom", "withr", "xfun", "XML", "xml2", "yaml" ], "_vignettes": [ { "source": "introduction.Rmd", "filename": "introduction.html", "title": "A guide to use the Polytect: an automatic clustering and labeling method for multi-color digital PCR data", "author": "Yao Chen", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Examples", "Session Information", "References" ], "created": "2024-06-19 13:56:50", "modified": "2024-11-15 21:03:27", "commits": 12 } ], "_score": 4, "_indexed": true, "_nocasepkg": "polytect", "_universes": [ "bioc", "emmachenlingo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.5.0", "date": "2026-10-10T17:46:03.000Z", "distro": "resolute", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/2534358ad745a88596ed56ae4599fd0a61eb2a4507b1e11f116e21eed56b349f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.6.1", "os": "linux", "version": "1.5.0", "date": "2026-10-10T17:46:21.000Z", "distro": "resolute", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/3d768fb0eae8aa25184fb00c58e866510c85185410b40f0680b2b268a0c4b80c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.5.3", "os": "mac", "version": "1.5.0", "date": "2026-10-10T19:04:46.000Z", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/8b3f1ec32703998e114234cfbd5dcdce01dbd14c6e98d946ed90bbb30e12ddde", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.6.1", "os": "mac", "version": "1.5.0", "date": "2026-10-10T19:04:32.000Z", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/112dfb9e3e756fc3ff6f591332597bc12266d85585da8ba260949df8b04172ba", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.6.0", "os": "wasm", "version": "1.5.0", "date": "2026-10-10T17:45:13.000Z", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/90e6b6df25dbb6bfe68e070669c39c8138fb48bbe828afa2657d5c507b978bb3", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.7.0", "os": "win", "version": "1.5.0", "date": "2026-10-10T17:44:35.000Z", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/b5220a413a76ed6e07ba6a68910791d2618380374d9a6237deeaeb6c937d96a5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.5.3", "os": "win", "version": "1.5.0", "date": "2026-10-10T17:44:19.000Z", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/ad6f146c4146cbd3f3a5990145fb15b6b863cf224a8ffcf0ccdace4cf7d551ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" }, { "r": "4.6.1", "os": "win", "version": "1.5.0", "date": "2026-10-10T17:44:22.000Z", "commit": "48dacdd5c28012320783eaacc5393c42e200652a", "fileid": "https://r2.ropensci.org/5793f2a0ec941d172091198eaa71765dd388a4f501db11839bb5dd0fb3b9a557", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/38072478736" } ] }