{ "_id": "6a1937bcacfb0bcc41dd3087", "Package": "DropletUtils", "Version": "1.32.0", "Date": "2026-04-08", "Title": "Utilities for Handling Single-Cell Droplet Data", "Authors@R": "c(\nperson(\"Aaron\", \"Lun\", role = \"aut\"),\nperson(\"Jonathan\", \"Griffiths\", role=c(\"ctb\", \"cre\"), email = \"jonathan.griffiths.94@gmail.com\"),\nperson(\"Davis\", \"McCarthy\", role=\"ctb\"),\nperson(\"Dongze\", \"He\", role=\"ctb\"),\nperson(\"Rob\", \"Patro\", role=\"ctb\"))", "biocViews": "ImmunoOncology, SingleCell, Sequencing, RNASeq,\nGeneExpression, Transcriptomics, DataImport, Coverage", "Description": "Provides a number of utility functions for handling\nsingle-cell (RNA-seq) data from droplet technologies such as\n10X Genomics. This includes data loading from count matrices or\nmolecule information files, identification of cells from empty\ndroplets, removal of barcode-swapped pseudo-cells, and\ndownsampling of the count matrix.", "License": "GPL-3", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "SystemRequirements": "C++17, GNU make", "RoxygenNote": "7.3.2", "Encoding": "UTF-8", "Config/pak/sysreqs": "make libssl-dev zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:47:06 UTC", "RemoteUrl": "https://github.com/bioc/DropletUtils", "RemoteRef": "RELEASE_3_23", "RemoteSha": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "Packaged": { "Date": "2026-05-29 06:12:30 UTC", "User": "root" }, "Author": "Aaron Lun [aut],\nJonathan Griffiths [ctb, cre],\nDavis McCarthy [ctb],\nDongze He [ctb],\nRob Patro [ctb]", "Maintainer": "Jonathan Griffiths ", "MD5sum": "a4af9142c51b9ef57ef1c4fdecc4948f", "_user": "bioc-release", "_type": "src", "_file": "DropletUtils_1.32.0.tar.gz", "_fileid": "7fe4c798fb1f5b3a20dadd287710d09d8cac326f9c6c6eeee749517132b4e152", "_filesize": 668556, "_sha256": "7fe4c798fb1f5b3a20dadd287710d09d8cac326f9c6c6eeee749517132b4e152", "_created": "2026-05-29T06:12:30.000Z", "_published": "2026-05-29T06:52:44.831Z", "_jobs": [ { "job": 78448028005, "time": 229, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7284349604" }, { "job": 78448028026, "time": 409, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7284391746" }, { "job": 78448028057, "time": 500, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7284413351" }, { "job": 78448028035, "time": 445, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7284400295" }, { "job": 78448028014, "time": 512, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7284415901" }, { "job": 78448028024, "time": 303, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7284725127" }, { "job": 78448028032, "time": 783, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7284837413" }, { "job": 78448028023, "time": 277, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7284717007" }, { "job": 78448028050, "time": 634, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7284800950" }, { "job": 78447367472, "time": 352, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284296873" }, { "job": 78448027999, "time": 193, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 78448028020, "time": 1488, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7284644042" }, { "job": 78448028017, "time": 1343, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7284610537" }, { "job": 78448028033, "time": 1484, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7284643015" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/DropletUtils", "_commit": { "id": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380426 }, "_maintainer": { "name": "Jonathan Griffiths", "email": "jonathan.griffiths.94@gmail.com", "login": "jonathangriffiths", "description": "CTO, Cyclana Bio", "uuid": 7976085 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "SingleCellExperiment", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "beachmat", "role": "LinkingTo" }, { "package": "assorthead", "role": "LinkingTo" }, { "package": "Rhdf5lib", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "dqrng", "role": "LinkingTo" }, { "package": "scuttle", "role": "LinkingTo" }, { "package": "utils", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "IRanges", "role": "Imports" }, { "package": "GenomicRanges", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "SparseArray", "version": ">= 1.5.18", "role": "Imports" }, { "package": "DelayedArray", "version": ">= 0.31.9", "role": "Imports" }, { "package": "DelayedMatrixStats", "role": "Imports" }, { "package": "HDF5Array", "role": "Imports" }, { "package": "rhdf5", "role": "Imports" }, { "package": "edgeR", "role": "Imports" }, { "package": "R.utils", "role": "Imports" }, { "package": "dqrng", "role": "Imports" }, { "package": "beachmat", "role": "Imports" }, { "package": "scuttle", "version": ">= 1.21.4", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "DropletTestFiles", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 13, "_updates": [ { "week": "2025-22", "n": 1 }, { "week": "2025-24", "n": 2 }, { "week": "2025-27", "n": 1 }, { "week": "2025-33", "n": 3 }, { "week": "2025-34", "n": 2 }, { "week": "2025-35", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-15", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.33.0", "bioc": "3.24" }, { "branch": "release", "version": "1.32.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "singlecell", "sequencing", "rnaseq", "geneexpression", "transcriptomics", "dataimport", "coverage", "curl", "openssl", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 4636, "source": "https://www.bioconductor.org/packages/stats/bioc/DropletUtils" }, "_mentions": 14, "_searchresults": 3408, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/DropletUtils.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "ambientContribMaximum", "ambientContribNegative", "ambientContribSparse", "ambientProfileBimodal", "ambientProfileEmpty", "barcodeRanks", "chimericDrops", "cleanTagCounts", "controlAmbience", "defaultDrops", "downsampleBatches", "downsampleMatrix", "downsampleReads", "emptyDrops", "emptyDropsCellRanger", "encodeSequences", "estimateAmbience", "get10xMolInfoStats", "hashedDrops", "inferAmbience", "makeCountMatrix", "maximumAmbience", "read10xCounts", "read10xMolInfo", "removeAmbience", "removeChimericDrops", "removeSwappedDrops", "swappedDrops", "testEmptyDrops", "write10xCounts" ], "_help": [ { "page": "ambientContribMaximum", "title": "Ambient contribution by maximum scaling", "topics": [ "ambientContribMaximum", "ambientContribMaximum,ANY-method", "ambientContribMaximum,SummarizedExperiment-method", "maximumAmbience" ] }, { "page": "ambientContribNegative", "title": "Ambient contribution from negative controls", "topics": [ "ambientContribNegative", "ambientContribNegative,ANY-method", "ambientContribNegative,SummarizedExperiment-method", "controlAmbience" ] }, { "page": "ambientContribSparse", "title": "Ambient contribution by assuming sparsity", "topics": [ "ambientContribSparse", "ambientContribSparse,ANY-method", "ambientContribSparse,SummarizedExperiment-method" ] }, { "page": "ambientProfileBimodal", "title": "Ambient profile from bimodality", "topics": [ "ambientProfileBimodal", "ambientProfileBimodal,ANY-method", "ambientProfileBimodal,SummarizedExperiment-method", "inferAmbience" ] }, { "page": "ambientProfileEmpty", "title": "Estimate the ambient profile from empty droplets", "topics": [ "ambientProfileEmpty", "ambientProfileEmpty,ANY-method", "ambientProfileEmpty,SummarizedExperiment-method", "estimateAmbience" ] }, { "page": "barcodeRanks", "title": "Calculate barcode ranks", "topics": [ "barcodeRanks", "barcodeRanks,ANY-method", "barcodeRanks,SummarizedExperiment-method" ] }, { "page": "chimericDrops", "title": "Remove chimeric molecules", "topics": [ "chimericDrops", "removeChimericDrops" ] }, { "page": "cleanTagCounts", "title": "Clean a tag-based dataset", "topics": [ "cleanTagCounts", "cleanTagCounts,ANY-method", "cleanTagCounts,SummarizedExperiment-method" ] }, { "page": "defaultDrops", "title": "Call cells from their total number of UMIs", "topics": [ "defaultDrops", "defaultDrops,ANY-method", "defaultDrops,SummarizedExperiment-method" ] }, { "page": "downsampleReads", "title": "Downsample reads in a 10X Genomics dataset", "topics": [ "downsampleReads" ] }, { "page": "emptyDrops", "title": "Identify empty droplets", "topics": [ "emptyDrops", "emptyDrops,ANY-method", "emptyDrops,SummarizedExperiment-method", "testEmptyDrops" ] }, { "page": "emptyDropsCellRanger", "title": "CellRanger's emptyDrops variant", "topics": [ "emptyDropsCellRanger", "emptyDropsCellRanger,ANY-method", "emptyDropsCellRanger,SummarizedExperiment-method" ] }, { "page": "encodeSequences", "title": "Encode nucleotide sequences", "topics": [ "encodeSequences" ] }, { "page": "get10xMolInfoStats", "title": "Get 10x cell statistics", "topics": [ "get10xMolInfoStats" ] }, { "page": "hashedDrops", "title": "Demultiplex cell hashing data", "topics": [ "hashedDrops", "hashedDrops,ANY-method", "hashedDrops,SummarizedExperiment-method" ] }, { "page": "makeCountMatrix", "title": "Make a count matrix", "topics": [ "makeCountMatrix" ] }, { "page": "read10xCounts", "title": "Load data from a 10X Genomics experiment", "topics": [ "read10xCounts" ] }, { "page": "read10xMolInfo", "title": "Read the 10X molecule information file", "topics": [ "read10xMolInfo" ] }, { "page": "removeAmbience", "title": "Remove the ambient profile", "topics": [ "removeAmbience", "removeAmbience,ANY-method", "removeAmbience,SummarizedExperiment-method" ] }, { "page": "swappedDrops", "title": "Clean barcode-swapped droplet data", "topics": [ "removeSwappedDrops", "swappedDrops" ] }, { "page": "write10xCounts", "title": "Write count data in the 10x format", "topics": [ "write10xCounts" ] } ], "_readme": "https://github.com/bioc/DropletUtils/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "assorthead", "beachmat", "BH", "Biobase", "BiocGenerics", "biocmake", "BiocParallel", "codetools", "cpp11", "DelayedArray", "DelayedMatrixStats", "dir.expiry", "dqrng", "edgeR", "filelock", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "h5mread", "HDF5Array", "IRanges", "lambda.r", "lattice", "limma", "locfit", "Matrix", "MatrixGenerics", "matrixStats", "R.methodsS3", "R.oo", "R.utils", "Rcpp", "rhdf5", "rhdf5filters", "Rhdf5lib", "S4Arrays", "S4Vectors", "scuttle", "Seqinfo", "SingleCellExperiment", "sitmo", "snow", "SparseArray", "sparseMatrixStats", "statmod", "SummarizedExperiment", "XVector" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.5.0-2ubuntu10.9", "name": "curl", "homepage": "https://curl.se/", "description": "easy-to-use client-side URL transfer library (OpenSSL flavour)" }, { "shlib": "libcrypto", "package": "libssl3t64", "headers": "libssl-dev", "source": "openssl", "version": "3.0.13-0ubuntu3.9", "name": "openssl", "homepage": "https://www.openssl.org/", "description": "Secure Sockets Layer toolkit - shared libraries" }, { "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": "DropletUtils.Rmd", "filename": "DropletUtils.html", "title": "Utilities for handling droplet-based single-cell RNA-seq data", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Reading in 10X Genomics data", "From the UMI count matrix", "From the molecule information file", "Downsampling on the reads", "Computing barcode ranks", "Detecting empty droplets", "Demultiplexing hashed libraries", "Removing swapping effects", "Barcode swapping between samples", "Chimeric reads within cells", "Session information" ], "created": "2017-12-21 11:22:25", "modified": "2020-07-15 07:42:16", "commits": 14 } ], "_score": 10.442920134188064, "_indexed": false, "_nocasepkg": "dropletutils", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/DropletUtils", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.32.0", "date": "2026-05-29T06:16:16.000Z", "distro": "noble", "arch": "aarch64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "2618c4d705d5cd56f3e00e095bc91a4869c2158214f3a702672e364dcf5a1099", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.7.0", "os": "linux", "version": "1.32.0", "date": "2026-05-29T06:17:33.000Z", "distro": "noble", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "c1bee6f9a0c4f77de31ebf1ae640407930d0923dd20775d2b7e4ac8df9fb06cd", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.6.0", "os": "linux", "version": "1.32.0", "date": "2026-05-29T06:16:31.000Z", "distro": "noble", "arch": "aarch64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "b138fd4b0f28ea65f15c6965075834d32fa294f0c2058bb8b29bcaaeea51b993", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.6.0", "os": "linux", "version": "1.32.0", "date": "2026-05-29T06:17:22.000Z", "distro": "noble", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "af82a1134edbe352dc6a8317896e68afb221f7364ef64e9b16d9be939778c660", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.5.3", "os": "mac", "version": "1.32.0", "date": "2026-05-29T06:41:07.000Z", "arch": "aarch64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "99ddee83a190f8bbc9ec34344f545773568052e3bba6a86203311a9ef950520e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.5.3", "os": "mac", "version": "1.32.0", "date": "2026-05-29T06:43:16.000Z", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "15e3027598080d44aec8391cd65616b75e1eeebd2bebf43c97aa378cd6058eab", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.6.0", "os": "mac", "version": "1.32.0", "date": "2026-05-29T06:40:36.000Z", "arch": "aarch64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "0edd385c926fef78ad2d78d0119561d72ce8431f7a791bb36a1567a3be19a9bc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.6.0", "os": "mac", "version": "1.32.0", "date": "2026-05-29T06:42:56.000Z", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "9a78580689d9f61103216494ba06079ad383da3ccebc920390632a35c900c29f", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.7.0", "os": "win", "version": "1.32.0", "date": "2026-05-29T06:30:55.000Z", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "fd2b2f3e31fa5cf6755e10777a75b8d9bf841d7b80cc14685197aabb5c57c5ce", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.5.3", "os": "win", "version": "1.32.0", "date": "2026-05-29T06:28:39.000Z", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "89dd1f332f200e9b73b4e4b11877dbd4a545a1e7b4770da694868a9f9ad8f527", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" }, { "r": "4.6.0", "os": "win", "version": "1.32.0", "date": "2026-05-29T06:30:32.000Z", "arch": "x86_64", "commit": "5f828e002a81a014b71bd0c9f586f3a3a1e8f34d", "fileid": "7430391814cd827305b731d80a0772b37f605d92f50fcfb2a24c592657d1106e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26621209650" } ] }