{ "_id": "6a1861feacfb0bcc41dbe7f8", "Package": "recall", "Title": "Calibrated Clustering with Artificial Variables to Avoid\nOver-Clustering in Single-Cell RNA-Sequencing", "Version": "0.1.0", "Authors@R": "person(\"Zaoqu\", \"Liu\", , \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0452-742X\"))", "Description": "recall (Calibrated Clustering with Artificial Variables)\nis a method for protecting against over-clustering by\ncontrolling for the impact of double-dipping. The approach can\nbe applied to any clustering algorithm (implemented are the\nLouvain and Leiden algorithms with plans for K-means, and\nhierarchical clustering algorithms). The method provides\nstate-of-the-art clustering performance and can rapidly analyze\nlarge-scale scRNA-seq studies and is compatible with the Seurat\nlibrary (V4 and V5).", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "License": "MIT + file LICENSE", "Remotes": [ "scDesign3=github::SONGDONGYUAN1994/scDesign3" ], "VignetteBuilder": "knitr", "URL": "https://zaoqu-liu.github.io/recall/,\nhttps://github.com/Zaoqu-Liu/recall", "BugReports": "https://github.com/Zaoqu-Liu/recall/issues", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-23 18:03:47 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/recall", "RemoteRef": "main", "RemoteSha": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 14:58:11 UTC", "User": "root" }, "Author": "Zaoqu Liu [aut, cre] (ORCID: )", "Maintainer": "Zaoqu Liu ", "MD5sum": "f9841b2015af2b75f2cc3ab955410762", "_user": "zaoqu-liu", "_type": "src", "_file": "recall_0.1.0.tar.gz", "_fileid": "a4c96b66e255d47e53d5c523575089b745862358170beb92dc814de3cea62ae0", "_filesize": 433144, "_sha256": "a4c96b66e255d47e53d5c523575089b745862358170beb92dc814de3cea62ae0", "_created": "2026-05-28T14:58:11.000Z", "_published": "2026-05-28T15:40:46.302Z", "_distro": "noble", "_jobs": [ { "job": 78320107655, "time": 245, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7269450916" }, { "job": 78320107816, "time": 200, "config": "linux-release-x86_64", "r": "4.6.0", "check": "ERROR", "artifact": "7269454255" }, { "job": 78320107792, "time": 112, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "ERROR", "artifact": "7270353797" }, { "job": 78320107904, "time": 89, "config": "macos-release-arm64", "r": "4.6.0", "check": "ERROR", "artifact": "7270304797" }, { "job": 78318886675, "time": 255, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7269300359" }, { "job": 78320107653, "time": 208, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7269442863" }, { "job": 78320107819, "time": 135, "config": "windows-devel", "r": "4.7.0", "check": "ERROR", "artifact": "7269413915" }, { "job": 78320107749, "time": 310, "config": "windows-oldrel", "r": "4.5.3", "check": "ERROR", "artifact": "7269522217" }, { "job": 78320107765, "time": 134, "config": "windows-release", "r": "4.6.0", "check": "ERROR", "artifact": "7269414578" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/recall", "_commit": { "id": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "author": "LIU Zaoqu <68080738+Zaoqu-Liu@users.noreply.github.com>", "committer": "GitHub ", "message": "Update README.md", "time": 1769191427 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "orcid": "0000-0002-0452-742X", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "Matrix", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.0.0", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "scDesign3", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "fitdistrplus", "role": "Imports" }, { "package": "lamW", "role": "Imports" }, { "package": "knockoff", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "countsplit", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" } ], "_owner": "zaoqu-liu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 3 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "zaoqu-liu", "count": 3, "uuid": 68080738 } ], "_userbio": { "uuid": 68080738, "type": "user", "name": "LIU Zaoqu", "description": "AI4S" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/recall" }, "_devurl": "https://github.com/zaoqu-liu/recall", "_pkgdown": "https://zaoqu-liu.github.io/recall/", "_searchresults": 32, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/recall.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "FindClustersCountsplit", "FindClustersRecall", "seurat_workflow" ], "_help": [ { "page": "compute_knockoff_filter", "title": "Returns the genes selected by the knockoff filter", "topics": [ "compute_knockoff_filter" ] }, { "page": "estimate_negative_binomial", "title": "Maximum likelihood estimation for the negative binomial distribution.", "topics": [ "estimate_negative_binomial" ] }, { "page": "estimate_negative_binomial_copula", "title": "todo", "topics": [ "estimate_gaussian_copula", "estimate_negative_binomial_copula", "estimate_poisson_copula", "estimate_zi_poisson_copula" ] }, { "page": "estimate_zi_poisson", "title": "Maximum likelihood estimation for the zero-inflated Poisson distribution with Poisson parameter lambda and zero proportion prop.zero.", "topics": [ "estimate_zi_poisson" ] }, { "page": "FindClustersCountsplit", "title": "Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).", "topics": [ "FindClustersCountsplit" ] }, { "page": "FindClustersRecall", "title": "Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).", "topics": [ "FindClustersRecall" ] }, { "page": "get_seurat_obj_with_artificial_variables", "title": "Returns a Seurat object that contains additional (fake) RNA expression counts.", "topics": [ "get_seurat_obj_with_artificial_variables" ] }, { "page": "rzipoisson", "title": "Random data generation for the zero-infalted Poisson distribution with Poisson parameter lambda and zero proportion prop.zero.", "topics": [ "rzipoisson" ] }, { "page": "seurat_workflow", "title": "Runs a typical Seurat workflow on a Seurat object (up to dimensionality reduction and clustering).", "topics": [ "seurat_workflow" ] } ], "_readme": "https://github.com/Zaoqu-Liu/recall/raw/main/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "bitops", "bslib", "cachem", "caTools", "cli", "cluster", "codetools", "commonmark", "coop", "corpcor", "countsplit", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "deldir", "digest", "dotCall64", "dplyr", "dqrng", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "gamlss", "gamlss.data", "gamlss.dist", "generics", "GenomicRanges", "ggplot2", "ggrepel", "ggridges", "glmnet", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "IRanges", "irlba", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "knockoff", "labeling", "lambda.r", "lamW", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lmtest", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mclust", "memoise", "mgcv", "mime", "miniUI", "mvtnorm", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pbmcapply", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "progressr", "promises", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppParallel", "RcppProgress", "RcppTOML", "Rdsdp", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scattermore", "scDesign3", "sctransform", "Seqinfo", "Seurat", "SeuratObject", "shape", "shiny", "SingleCellExperiment", "sitmo", "snow", "sourcetools", "sp", "spam", "SparseArray", "sparseMVN", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tensor", "tibble", "tidyr", "tidyselect", "tinytex", "umap", "utf8", "uwot", "vctrs", "viridis", "viridisLite", "withr", "xfun", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "advanced-usage.Rmd", "filename": "advanced-usage.html", "title": "Advanced Usage", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Null Distribution Selection", "Available Methods", "Choosing the Right Method", "Assessing Data Characteristics", "Parallel Computing", "Cross-Platform Configuration", "Memory Management", "Count Splitting Alternative", "Method Comparison", "Resolution Tuning", "Iterative Resolution Reduction", "Finding Optimal Starting Resolution", "Clustering Algorithm Selection", "Louvain vs Leiden", "Integration with Seurat Workflow", "Complete Analysis Pipeline", "Using seurat_workflow Helper", "Batch Processing Multiple Samples", "Troubleshooting", "Common Issues", "Session Information" ], "created": "2026-01-23 17:58:35", "modified": "2026-01-23 17:58:35", "commits": 1 }, { "source": "methodology.Rmd", "filename": "methodology.html", "title": "Algorithm and Methodology", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The Double-Dipping Problem", "Mathematical Framework", "The Knockoff Filter", "The W Statistic", "FDR-Controlled Selection", "The recall Algorithm", "Stage 1: Synthetic Null Variable Generation", "Supported Distributions", "Stage 2: Joint Analysis", "Stage 3: Iterative Calibration", "Zero-Inflated Poisson Estimation", "Maximum Likelihood Estimation", "Implementation", "Negative Binomial Estimation", "Copula Models", "Gaussian Copula", "Theoretical Guarantees", "FDR Control", "Comparison with Count Splitting", "References" ], "created": "2026-01-23 17:58:35", "modified": "2026-01-23 17:58:35", "commits": 1 }, { "source": "basic-usage.Rmd", "filename": "basic-usage.html", "title": "Basic Usage", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup", "Loading Data", "Standard Preprocessing", "Running recall", "Accessing Results", "Visualization", "Comparison with Standard Clustering", "Next Steps", "Session Info" ], "created": "2026-01-23 17:46:08", "modified": "2026-01-23 17:58:35", "commits": 2 }, { "source": "visualization.Rmd", "filename": "visualization.html", "title": "Visualization Guide", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup", "Data Preparation", "Comparing Clustering Methods", "Standard vs Calibrated Clustering", "Side-by-Side UMAP Comparison", "Cluster Quality Assessment", "Cluster Size Distribution", "Marker Gene Heatmap", "Feature Visualization", "Expression Patterns", "Violin Plots", "Resolution Analysis", "Multi-Resolution Comparison", "Publication-Ready Figures", "Custom Theme", "Exporting Figures", "Session Info" ], "created": "2026-01-23 17:58:35", "modified": "2026-01-23 17:58:35", "commits": 1 } ], "_score": 3.8061799739838875, "_indexed": true, "_nocasepkg": "recall", "_universes": [ "zaoqu-liu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.0", "date": "2026-05-28T15:03:42.000Z", "distro": "noble", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "877fde34296b39e6eea2912d73e2e28d442cb78f6bdb4993b1b8b112440364e0", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.6.0", "os": "linux", "version": "0.1.0", "date": "2026-05-28T15:03:50.000Z", "distro": "noble", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "caddfd45eb5f166dfa35595b76553cbb7cdd33b76153e4a2186da39999f1754e", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.5.3", "os": "mac", "version": "0.1.0", "date": "2026-05-28T15:39:57.000Z", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "2b8a117cdd4bb4361e9707c9ec8c19665d371f0a665cac5b843c7e583d80503a", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.6.0", "os": "mac", "version": "0.1.0", "date": "2026-05-28T15:38:01.000Z", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "212cce6f4a9dcfa42dc460efe3138a820d83faaea335e96cd74d5dd4a5152121", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.0", "date": "2026-05-28T15:03:54.000Z", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "7487d2d2d121e4736996588c5ec102dcc99d2d1ef7ff039b3f82fb9ae1394366", "status": "success", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.7.0", "os": "win", "version": "0.1.0", "date": "2026-05-28T15:02:11.000Z", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "07cd6f275047cf2c9f48d7025494c70fdf1d6c0565676b2066551ac2779eee34", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.5.3", "os": "win", "version": "0.1.0", "date": "2026-05-28T15:06:12.000Z", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "041adb52c111938ed26b75fcd2f5f33100f40e83e13def2dbc6efd71737487d4", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" }, { "r": "4.6.0", "os": "win", "version": "0.1.0", "date": "2026-05-28T15:02:11.000Z", "commit": "ebad0cdf9754bb32a3a756d5af31e7df8fad97c3", "fileid": "4c8732209723a58ea941414091809da862d01ce8c1084b314203855b4ce2da68", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26582227690" } ] }