{ "_id": "6a17e100acfb0bcc41d9f179", "Package": "demuxmix", "Title": "Demultiplexing oligo-barcoded scRNA-seq data using regression\nmixture models", "Version": "1.15.0", "Date": "2024-01-29", "Description": "A package for demultiplexing single-cell sequencing\nexperiments of pooled cells labeled with barcode\noligonucleotides. The package implements methods to fit\nregression mixture models for a probabilistic classification of\ncells, including multiplet detection. Demultiplexing error\nrates can be estimated, and methods for quality control are\nprovided.", "Authors@R": "person(\"Hans-Ulrich\", \"Klein\",\nemail = \"hansulrich.klein@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-6382-9428\"))", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "biocViews": "SingleCell, Sequencing, Preprocessing, Classification,\nRegression", "BiocType": "Software", "URL": "https://github.com/huklein/demuxmix", "BugReports": "https://github.com/huklein/demuxmix/issues", "Encoding": "UTF-8", "RoxygenNote": "7.2.2", "Config/testthat/edition": "3", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:58:56 UTC", "RemoteUrl": "https://github.com/bioc/demuxmix", "RemoteRef": "HEAD", "RemoteSha": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 06:25:14 UTC", "User": "root" }, "Author": "Hans-Ulrich Klein [aut, cre] (ORCID:\n)", "Maintainer": "Hans-Ulrich Klein ", "MD5sum": "2c26696540b5ee8997dd054733c0de87", "_user": "bioc", "_type": "src", "_file": "demuxmix_1.15.0.tar.gz", "_fileid": "55994f16c8b4611b3557f3e5ae41c102802939bc9a3bda247c19674717c7cb66", "_filesize": 1351926, "_sha256": "55994f16c8b4611b3557f3e5ae41c102802939bc9a3bda247c19674717c7cb66", "_created": "2026-05-28T06:25:14.000Z", "_published": "2026-05-28T06:30:24.029Z", "_jobs": [ { "job": 78235762721, "time": 170, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7259132446" }, { "job": 78235762694, "time": 251, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7259151638" }, { "job": 78235762682, "time": 205, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7259140770" }, { "job": 78235762685, "time": 98, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7259140771" }, { "job": 78235762692, "time": 151, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7259154078" }, { "job": 78235184384, "time": 293, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7259091924" }, { "job": 78235762727, "time": 142, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7259126414" }, { "job": 78235762719, "time": 160, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7259130260" }, { "job": 78235762744, "time": 130, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7259123433" }, { "job": 78235762686, "time": 121, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7259121380" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 8 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/demuxmix", "_commit": { "id": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381136 }, "_maintainer": { "name": "Hans-Ulrich Klein", "email": "hansulrich.klein@gmail.com", "login": "huklein", "description": "I am a bioinformatician interested in computational neuroimmunology working at Columbia University.", "uuid": 29508973, "orcid": "0000-0002-6382-9428" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "DropletUtils", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.15.0", "bioc": "3.24" }, { "branch": "release", "version": "1.14.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "sequencing", "preprocessing", "classification", "regression" ], "_stars": 5, "_contributors": [ { "user": "huklein", "count": 57, "uuid": 29508973 }, { "user": "jwokaty", "count": 6, "uuid": 1744257 }, { "user": "petehaitch", "count": 1, "uuid": 1049741 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 438, "source": "https://www.bioconductor.org/packages/stats/bioc/demuxmix" }, "_devurl": "https://github.com/huklein/demuxmix", "_searchresults": 27, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/demuxmix.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/huklein/demuxmix", "_realowner": "bioc", "_cranurl": false, "_exports": [ "demuxmix", "dmmClassify", "dmmOverlap", "dmmSimulateHto", "pAcpt", "pAcpt<-", "plotDmmHistogram", "plotDmmPosteriorP", "plotDmmScatter", "summary" ], "_datasets": [ { "name": "csf", "title": "Hashtag oligonucleotide (HTO) counts from 2,590 droplets", "object": "csf", "file": "csf.RData", "class": [ "data.frame" ], "fields": [ "HTO", "NumGenes", "freemuxlet", "freemuxlet.prob" ], "rows": 2590, "table": true, "tojson": true } ], "_help": [ { "page": "csf", "title": "Hashtag oligonucleotide (HTO) counts from 2,590 droplets", "topics": [ "csf" ] }, { "page": "demuxmix", "title": "Demultiplexing using mixture models", "topics": [ "demuxmix", "demuxmix,Matrix,missing-method", "demuxmix,matrix,missing-method", "demuxmix,Matrix,numeric-method", "demuxmix,matrix,numeric-method" ] }, { "page": "Demuxmix-class", "title": "A class representing a set of mixture models fitted to HTO data", "topics": [ "Demuxmix", "Demuxmix-class", "pAcpt", "pAcpt,Demuxmix-method", "pAcpt<-", "pAcpt<-,Demuxmix,numeric-method", "show,Demuxmix-method", "summary,Demuxmix-method" ] }, { "page": "dmmClassify", "title": "Return classification results from a Demuxmix object", "topics": [ "dmmClassify", "dmmClassify,Demuxmix-method" ] }, { "page": "dmmOverlap", "title": "Calculate the intersection of two components of a mixture model", "topics": [ "dmmOverlap", "dmmOverlap,Demuxmix,ANY-method", "dmmOverlap,Demuxmix,missing-method" ] }, { "page": "dmmSimulateHto", "title": "Simulate HTO sequencing data", "topics": [ "dmmSimulateHto", "dmmSimulateHto,matrix-method" ] }, { "page": "plotDmmHistogram", "title": "Plotting a histogram with mixture probability mass function", "topics": [ "plotDmmHistogram", "plotDmmHistogram,Demuxmix,ANY-method", "plotDmmHistogram,Demuxmix,missing-method" ] }, { "page": "plotDmmPosteriorP", "title": "Plotting a histogram of posterior probabilities", "topics": [ "plotDmmPosteriorP", "plotDmmPosteriorP,Demuxmix,ANY-method", "plotDmmPosteriorP,Demuxmix,missing-method" ] }, { "page": "plotDmmScatter", "title": "Plotting RNA features versus HTO counts", "topics": [ "plotDmmScatter", "plotDmmScatter,Demuxmix,ANY-method", "plotDmmScatter,Demuxmix,missing-method" ] }, { "page": "summary", "title": "Summarize classification results of a Demuxmix model", "topics": [ "summary", "summary,data.frame-method" ] } ], "_readme": "https://github.com/bioc/demuxmix/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "farver", "ggplot2", "glue", "gridExtra", "gtable", "isoband", "labeling", "lattice", "lifecycle", "MASS", "Matrix", "R6", "RColorBrewer", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "demuxmix.Rmd", "filename": "demuxmix.html", "title": "Demultiplexing oligonucleotide-labeled scRNA-seq data with demuxmix", "author": "Hans-Ulrich Klein", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Quick start", "Demultiplexing droplets with demuxmix", "Example datasets", "Simulated dataset", "Cell line mixture dataset", "Running demuxmix", "Quality control", "Comparison to hashedDrops", "Special usecase: pooling non-labeled with labeled cells", "Session Info", "References" ], "created": "2021-08-08 16:05:27", "modified": "2022-09-07 00:23:51", "commits": 15 } ], "_score": 5.9084850188786495, "_indexed": true, "_nocasepkg": "demuxmix", "_universes": [ "bioc", "huklein" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.15.0", "date": "2026-05-28T06:29:02.000Z", "distro": "noble", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "8fabfb424d80336363e212a32ad2431529446c6d6c649f0adf371d6f1e010b2c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.6.0", "os": "linux", "version": "1.15.0", "date": "2026-05-28T06:28:23.000Z", "distro": "noble", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "6e055741b325a4416c47fb0b0fc241e9f8183a52a37dff4d85b40a50f644c9a6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.5.3", "os": "mac", "version": "1.15.0", "date": "2026-05-28T06:28:41.000Z", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "78a1b915e78aba33ac92d884aad2f16ea93dab29f4d7d8ee4b486f9fea01e6f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.6.0", "os": "mac", "version": "1.15.0", "date": "2026-05-28T06:29:21.000Z", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "f07f7d871fc67aa764952dae44c0ce99912df9b8d4694bd2d12e376294c28bde", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.6.0", "os": "wasm", "version": "1.15.0", "date": "2026-05-28T06:28:03.000Z", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "fc826d0177440c7a17f4be50131ac436d942b078cdc7bc7d43e0b1027d196095", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.7.0", "os": "win", "version": "1.15.0", "date": "2026-05-28T06:27:25.000Z", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "2bc76b410e30822ed5c27dc3f6be339815d5d1729b2b4013554fd0a989956e15", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.5.3", "os": "win", "version": "1.15.0", "date": "2026-05-28T06:26:56.000Z", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "0f71507b20004223cc6f827d8ba5fcd08054b98b0c74f29174820814db136b6f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" }, { "r": "4.6.0", "os": "win", "version": "1.15.0", "date": "2026-05-28T06:26:49.000Z", "commit": "0375c4ecbb1c6eb0c1bb1d2b979096826cc73c7d", "fileid": "dfbd1d7673b75c64dfac9a0a29ec2894e2bffe53b725edccfc9d14c63be59f2b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26558357750" } ] }