{ "_id": "6a1ab28c1d7bb097a09d5b9a", "Package": "PoDCall", "Type": "Package", "Title": "Positive Droplet Calling for DNA Methylation Droplet Digital PCR", "Version": "1.21.0", "Authors@R": "c(person(\"Hans Petter\", \"Brodal\", \nrole=c(\"aut\", \"cre\"),\nemail=\"h.p.brodal@ous-research.no\"),\nperson(\"Marine\", \"Jeanmougin\", role=\"aut\",\nemail=\"marine.jeanmougin@rr-research.no\"),\nperson(\"Guro Elisabeth\", \"Lind\", role=\"aut\",\nemail=\"g.e.lind@ibv.uio.no\"))", "Description": "Reads files exported from 'QX Manager or QuantaSoft'\ncontaining amplitude values from a run of ddPCR (96 well plate)\nand robustly sets thresholds to determine positive droplets for\neach channel of each individual well. Concentration and\nnormalized concentration in addition to other metrics is then\ncalculated for each well. Results are returned as a table,\noptionally written to file, as well as optional plots\n(scatterplot and histogram) for both channels per well written\nto file. The package includes a shiny application which\nprovides an interactive and user-friendly interface to the full\nfunctionality of PoDCall.", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "biocViews": "Classification, Epigenetics, ddPCR, DifferentialMethylation,\nCpGIsland, DNAMethylation,", "StagedInstall": "no", "Config/pak/sysreqs": "cmake make libuv1-dev libxml2-dev libx11-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:54:40 UTC", "RemoteUrl": "https://github.com/bioc/PoDCall", "RemoteRef": "HEAD", "RemoteSha": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:07:07 UTC", "User": "root" }, "Author": "Hans Petter Brodal [aut, cre],\nMarine Jeanmougin [aut],\nGuro Elisabeth Lind [aut]", "Maintainer": "Hans Petter Brodal ", "MD5sum": "7489cf292ec2879d9a6dc265650ee9b9", "_user": "bioc", "_type": "src", "_file": "PoDCall_1.21.0.tar.gz", "_fileid": "457f07ef32ea7bcc5f0f21a4188721193ead6de31612efed813e92ad77c2b792", "_filesize": 2986820, "_sha256": "457f07ef32ea7bcc5f0f21a4188721193ead6de31612efed813e92ad77c2b792", "_created": "2026-05-30T07:07:07.000Z", "_published": "2026-05-30T09:49:00.301Z", "_jobs": [ { "job": 78632382556, "time": 165, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7306343500" }, { "job": 78632382553, "time": 482, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7306380297" }, { "job": 78632382554, "time": 483, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7306380415" }, { "job": 78632382550, "time": 291, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7307220360" }, { "job": 78632382542, "time": 308, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7307221900" }, { "job": 78632199264, "time": 196, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306323927" }, { "job": 78632382519, "time": 127, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306338841" }, { "job": 78632382568, "time": 890, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7306427091" }, { "job": 78632382558, "time": 716, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7306408213" }, { "job": 78632382549, "time": 707, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7306406927" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 15 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/PoDCall", "_commit": { "id": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380880 }, "_maintainer": { "name": "Hans Petter Brodal", "email": "h.p.brodal@ous-research.no", "login": "hanspetterbrodal", "description": "", "uuid": 73332267 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5", "role": "Depends" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "mclust", "role": "Imports" }, { "package": "diptest", "role": "Imports" }, { "package": "rlist", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "DT", "role": "Imports" }, { "package": "LaplacesDemon", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-28", "n": 2 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "classification", "epigenetics", "ddpcr", "differentialmethylation", "cpgisland", "dnamethylation" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 286, "source": "https://www.bioconductor.org/packages/stats/bioc/PoDCall" }, "_mentions": 1, "_searchresults": 13, "_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/PoDCall.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "importAmplitudeData", "importSampleSheet", "podcallChannelPlot", "podcallDdpcr", "podcallHistogram", "podcallMultiplot", "podcallScatterplot", "podcallShiny", "podcallThresholds" ], "_datasets": [ { "name": "thrTable", "title": "PoDCall Example Threshold Table", "object": "thrTable", "file": "thrTable.rda", "class": [ "data.frame" ], "fields": [ "sample_id", "target_ch", "thr_target", "thr_ctrl", "pos_dr_target", "pos_dr_ctrl", "tot_droplets", "c_target", "c_ctrl", "c_norm_4Plex", "c_norm_sg", "q", "target_assay", "ctrl_assay", "ref_well" ], "rows": 5, "table": true, "tojson": true } ], "_help": [ { "page": "importAmplitudeData", "title": "importAmplitudeData", "topics": [ "importAmplitudeData" ] }, { "page": "importSampleSheet", "title": "importSampleSheet", "topics": [ "importSampleSheet" ] }, { "page": "podcallChannelPlot", "title": "podcallChannelPlot", "topics": [ "podcallChannelPlot" ] }, { "page": "podcallDdpcr", "title": "Positive Droplet Calling for ddPCR", "topics": [ "podcallDdpcr" ] }, { "page": "podcallHistogram", "title": "podcallHistogram", "topics": [ "podcallHistogram" ] }, { "page": "podcallMultiplot", "title": "podcallMultiplot", "topics": [ "podcallMultiplot" ] }, { "page": "podcallScatterplot", "title": "podcallScatterplot", "topics": [ "podcallScatterplot" ] }, { "page": "podcallShiny", "title": "PoDCall shiny launcher", "topics": [ "podcallShiny" ] }, { "page": "podcallThresholds", "title": "podcallThresholds", "topics": [ "podcallThresholds" ] }, { "page": "thrTable", "title": "PoDCall Example Threshold Table", "topics": [ "thrTable" ] } ], "_readme": "https://github.com/bioc/PoDCall/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bit", "bit64", "bslib", "cachem", "cli", "clipr", "commonmark", "cpp11", "crayon", "crosstalk", "data.table", "digest", "diptest", "DT", "evaluate", "farver", "fastmap", "fontawesome", "fs", "ggplot2", "glue", "gridExtra", "gtable", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "LaplacesDemon", "later", "lazyeval", "lifecycle", "magrittr", "mclust", "memoise", "mime", "otel", "pillar", "pkgconfig", "prettyunits", "progress", "promises", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "readr", "rlang", "rlist", "rmarkdown", "S7", "sass", "scales", "shiny", "shinyjs", "sourcetools", "tibble", "tidyselect", "tinytex", "tzdb", "utf8", "vctrs", "viridisLite", "vroom", "withr", "xfun", "XML", "xtable", "yaml" ], "_vignettes": [ { "source": "PoDCall.Rmd", "filename": "PoDCall.html", "title": "PoDCall: Positive Droplet Caller for DNA Methylation ddPCR", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Gaussian Mixture Models", "Input Data", "Installation", "Example / Usage", "Optional arguments", "sampleSheetFile", "B", "Q", "refwell", "nrChannels", "targetChannel", "controlChannel", "software", "resultsToFile", "plots", "resPath", "Threshold table columns", "sample_id", "thr_target", "thr_ctrl", "pos_dr_target", "pos_dr_ctrl", "tot_droplets", "c_target", "c_ctrl", "c_norm_4Plex", "c_norm_sg", "q", "target_assay", "ctrl_assay", "ref_well", "PoDCall functions", "importAmplitudeData()", "importSampleSheet()", "podcallThresholds()", "podcallChannelPlot()", "podcallScatterplot()", "podcallHistogram()", "podcallMultiplot()", "PoDCall shiny application", "PodCall example data", "Cell Line Amplitude Data", "Calculated Threshold Table", "Session info" ], "created": "2020-10-23 08:22:15", "modified": "2024-12-19 10:00:20", "commits": 15 } ], "_score": 4.290034611362518, "_indexed": true, "_nocasepkg": "podcall", "_universes": [ "bioc", "hanspetterbrodal" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T07:09:34.000Z", "distro": "noble", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "b793680363732517709df2a8b033291d1877fdbfeadb849d542dd0ecf168fc0e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.6.0", "os": "linux", "version": "1.21.0", "date": "2026-05-30T07:09:53.000Z", "distro": "noble", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "326e8593daa30c640fa4792e1d30fac00f9e9760e26fcdfd2cc6a4795bfa7f1a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.5.3", "os": "mac", "version": "1.21.0", "date": "2026-05-30T09:32:17.000Z", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "c58d5816104cc01ab5bc0251c5b888f8986aad622dcf6ab340db2095af5691de", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.6.0", "os": "mac", "version": "1.21.0", "date": "2026-05-30T09:32:23.000Z", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "e02c2a70350a1b1a63ffd040b479fc54406c547a794c7b5fb32c728463e6f8ec", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.6.0", "os": "wasm", "version": "1.21.0", "date": "2026-05-30T07:09:33.000Z", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "725ef4eabf54a570e55a54b839bfcd500f62c8d9af5fd9ca58471738d68e353e", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.7.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T07:08:28.000Z", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "c0f91a3f7c44debe726b858403fbce7b8091a7406e36af187daa925ed2dee7ea", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.5.3", "os": "win", "version": "1.21.0", "date": "2026-05-30T07:08:41.000Z", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "f15b712556fda313196ac54870e60bb5224851d97fda18c6876dd80a364d93db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" }, { "r": "4.6.0", "os": "win", "version": "1.21.0", "date": "2026-05-30T07:08:30.000Z", "commit": "0a2a05e99acdcc664ad592d2cfee130e154bc965", "fileid": "ef8e13276e7ab6541df8177413dcd9b0c3dea5c205a5081311878627851ba6a5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677587941" } ] }