{ "_id": "6a1ed45db401979e7340e181", "Package": "scrapper", "Version": "1.7.3", "Date": "2026-05-19", "Authors@R": "person(\"Aaron\", \"Lun\", role=c(\"cre\", \"aut\"), email=\"infinite.monkeys.with.keyboards@gmail.com\")", "Title": "Bindings to C++ Libraries for Single-Cell Analysis", "Description": "Implements R bindings to C++ code for analyzing\nsingle-cell (expression) data, mostly from various libscran\nlibraries. Each function performs an individual step in the\nsingle-cell analysis workflow, ranging from quality control to\nclustering and marker detection. Additional wrappers are\nprovided for easy construction of end-to-end workflows\ninvolving Bioconductor objects like SingleCellExperiments.", "License": "MIT + file LICENSE", "biocViews": "Normalization, RNASeq, Software, GeneExpression,\nTranscriptomics, SingleCell, BatchEffect, QualityControl,\nDifferentialExpression, FeatureExtraction, PrincipalComponent,\nClustering", "SystemRequirements": "C++17, GNU make", "URL": "https://github.com/libscran/scrapper", "BugReports": "https://github.com/libscran/scrapper/issues", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-19 09:34:26 UTC", "RemoteUrl": "https://github.com/bioc/scrapper", "RemoteRef": "HEAD", "RemoteSha": "defe76d3933ce25103f33e82d79745398f63d912", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-19 11:11:35 UTC", "User": "root" }, "Author": "Aaron Lun [cre, aut]", "Maintainer": "Aaron Lun ", "MD5sum": "a6dbf0fcd0c56d9d1c99dc16cbf1ce43", "_user": "bioc", "_type": "src", "_file": "scrapper_1.7.3.tar.gz", "_fileid": "7c042385cc2ff3e564538b79719aa3bcc4dd285721558d015fa9a5233bdd6909", "_filesize": 1591783, "_sha256": "7c042385cc2ff3e564538b79719aa3bcc4dd285721558d015fa9a5233bdd6909", "_created": "2026-05-19T11:11:35.000Z", "_published": "2026-06-02T13:02:21.840Z", "_jobs": [ { "job": 79075652725, "time": 428, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7082031484" }, { "job": 79075653346, "time": 658, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7082107850" }, { "job": 79075653124, "time": 832, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7082165222" }, { "job": 79075653309, "time": 660, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7082108533" }, { "job": 79075653119, "time": 757, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7082140683" }, { "job": 79075653194, "time": 168, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 79075653264, "time": 421, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "FAIL", "artifact": "" }, { "job": 79075653213, "time": 590, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7082159464" }, { "job": 79075652792, "time": 416, "config": "macos-release-x86_64", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79075652034, "time": 891, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7081888195" }, { "job": 79075652105, "time": 378, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79075652787, "time": 1674, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7082443603" }, { "job": 79075653374, "time": 1992, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7082547733" }, { "job": 79075653505, "time": 2056, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7082568831" } ], "_bioccheck": { "error": 0, "warning": 2, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scrapper", "_commit": { "id": "defe76d3933ce25103f33e82d79745398f63d912", "author": "LTLA ", "committer": "LTLA ", "message": "Bumped version and date, updated NEWS.\n", "time": 1779183266 }, "_maintainer": { "name": "Aaron Lun", "email": "infinite.monkeys.with.keyboards@gmail.com", "login": "ltla", "twitter": "@realAaronLun", "description": "(ノಠ益ಠ)ノ彡┻━┻\n", "uuid": 8166669 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "Rcpp", "role": "LinkingTo" }, { "package": "assorthead", "version": ">= 1.5.16", "role": "LinkingTo" }, { "package": "beachmat", "role": "LinkingTo" }, { "package": "BiocNeighbors", "role": "LinkingTo" }, { "package": "Rigraphlib", "role": "LinkingTo" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "role": "Imports" }, { "package": "beachmat", "version": ">= 2.25.1", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "SparseArray", "role": "Imports" }, { "package": "DelayedArray", "role": "Imports" }, { "package": "BiocNeighbors", "version": ">= 1.99.0", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "IRanges", "role": "Suggests" }, { "package": "SummarizedExperiment", "role": "Suggests" }, { "package": "SingleCellExperiment", "role": "Suggests" }, { "package": "scRNAseq", "role": "Suggests" }, { "package": "org.Mm.eg.db", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "igraph", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 6, "_updates": [ { "week": "2025-21", "n": 1 }, { "week": "2025-22", "n": 1 }, { "week": "2025-23", "n": 1 }, { "week": "2025-29", "n": 1 }, { "week": "2025-31", "n": 1 }, { "week": "2025-35", "n": 1 }, { "week": "2025-36", "n": 2 }, { "week": "2025-37", "n": 4 }, { "week": "2025-38", "n": 1 }, { "week": "2025-39", "n": 1 }, { "week": "2025-40", "n": 3 }, { "week": "2025-41", "n": 1 }, { "week": "2025-42", "n": 3 }, { "week": "2025-43", "n": 6 }, { "week": "2025-44", "n": 6 }, { "week": "2025-46", "n": 1 }, { "week": "2025-49", "n": 3 }, { "week": "2025-50", "n": 3 }, { "week": "2025-51", "n": 9 }, { "week": "2025-52", "n": 18 }, { "week": "2026-01", "n": 13 }, { "week": "2026-02", "n": 9 }, { "week": "2026-03", "n": 7 }, { "week": "2026-04", "n": 2 }, { "week": "2026-07", "n": 1 }, { "week": "2026-10", "n": 4 }, { "week": "2026-11", "n": 1 }, { "week": "2026-15", "n": 3 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 13 }, { "week": "2026-19", "n": 6 }, { "week": "2026-20", "n": 1 }, { "week": "2026-21", "n": 4 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.7.2", "bioc": "3.24" }, { "branch": "release", "version": "1.6.2", "bioc": "3.23" } ], "_topics": [ "normalization", "rnaseq", "software", "geneexpression", "transcriptomics", "singlecell", "batcheffect", "qualitycontrol", "differentialexpression", "featureextraction", "principalcomponent", "clustering", "openblas", "cpp" ], "_stars": 8, "_contributors": [ { "user": "ltla", "count": 218, "uuid": 8166669 }, { "user": "jwokaty", "count": 8, "uuid": 1744257 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 1180, "source": "https://www.bioconductor.org/packages/stats/bioc/scrapper" }, "_devurl": "https://github.com/libscran/scrapper", "_searchresults": 109, "_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/readme.html", "extra/readme.md", "extra/scrapper.html", "manual.pdf" ], "_homeurl": "https://github.com/libscran/scrapper", "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateAcrossCells", "aggregateAcrossCells.se", "aggregateAcrossCellsDefaults", "aggregateAcrossGenes", "aggregateAcrossGenes.se", "aggregateAcrossGenesDefaults", "aggregateColData", "analyze", "analyze.se", "buildSnnGraph", "buildSnnGraphDefaults", "centerSizeFactors", "centerSizeFactorsDefaults", "centerSpikeInFactors", "centerSpikeInFactorsDefaults", "chooseHighlyVariableGenes", "chooseHighlyVariableGenesDefaults", "choosePseudoCount", "choosePseudoCountDefaults", "chooseRnaHvgs.se", "chooseRnaHvgsWithSpikeIns.se", "clusterGraph", "clusterGraph.se", "clusterGraphDefaults", "clusterKmeans", "clusterKmeans.se", "clusterKmeansDefaults", "combineFactors", "computeAdtQcMetrics", "computeAdtQcMetricsDefaults", "computeBlockWeights", "computeBlockWeightsDefaults", "computeClrm1Factors", "computeClrm1FactorsDefaults", "computeCrisprQcMetrics", "computeCrisprQcMetricsDefaults", "computeRnaQcMetrics", "computeRnaQcMetricsDefaults", "computeRnaQcMetricsWithAltExps", "convertAnalyzeResults", "correctMnn", "correctMnn.se", "correctMnnDefaults", "countGroupsByBlock", "DelayedArray", "extract_array", "extract_sparse_array", "filterAdtQcMetrics", "filterCrisprQcMetrics", "filterRnaQcMetrics", "fitVarianceTrend", "fitVarianceTrendDefaults", "formatComputeAdtQcMetricsResult", "formatComputeCrisprQcMetricsResult", "formatComputeRnaQcMetricsResult", "formatModelGeneVariancesResult", "formatScoreMarkersResult", "getTestAdtData.se", "getTestCrisprData.se", "getTestRnaData.se", "initializeCpp", "is_sparse", "LogNormalizedMatrix", "LogNormalizedMatrixSeed", "modelGeneVariances", "modelGeneVariancesDefaults", "normalizeAdtCounts.se", "normalizeCounts", "normalizeCountsDefaults", "normalizeCrisprCounts.se", "normalizeRnaCounts.se", "normalizeRnaCountsWithSpikeIns.se", "previewMarkers", "quickAdtQc.se", "quickCrisprQc.se", "quickRnaQc.se", "reportGroupMarkerStatistics", "runAllNeighborSteps", "runAllNeighborSteps.se", "runPca", "runPca.se", "runPcaDefaults", "runTsne", "runTsne.se", "runTsneDefaults", "runUmap", "runUmap.se", "runUmapDefaults", "sanitizeSizeFactors", "sanitizeSizeFactorsDefaults", "scaleByNeighbors", "scaleByNeighbors.se", "scaleByNeighborsDefaults", "scoreGeneSet", "scoreGeneSet.se", "scoreGeneSetDefaults", "scoreMarkers", "scoreMarkers.se", "scoreMarkersDefaults", "subsampleByNeighbors", "subsampleByNeighborsDefaults", "subsampleByPartition", "subsampleByPartitionDefaults", "suggestAdtQcThresholds", "suggestAdtQcThresholdsDefaults", "suggestCrisprQcThresholds", "suggestCrisprQcThresholdsDefaults", "suggestRnaQcThresholds", "suggestRnaQcThresholdsDefaults", "summarizeEffects", "summarizeEffectsDefaults", "testEnrichment", "testEnrichmentDefaults", "tsnePerplexityToNeighbors", "type" ], "_help": [ { "page": "scrapper-package", "title": "scrapper: Bindings to C++ Libraries for Single-Cell Analysis", "topics": [ "scrapper-package", "scrapper" ] }, { "page": "adt_quality_control", "title": "Quality control for ADT count data", "topics": [ "adt_quality_control", "computeAdtQcMetrics", "filterAdtQcMetrics", "suggestAdtQcThresholds" ] }, { "page": "adt_quality_control_defaults", "title": "Default parameters for ADT quality control", "topics": [ "adt_quality_control_defaults", "computeAdtQcMetricsDefaults", "suggestAdtQcThresholdsDefaults" ] }, { "page": "aggregateAcrossCells", "title": "Aggregate expression across cells", "topics": [ "aggregateAcrossCells" ] }, { "page": "aggregateAcrossCells.se", "title": "Aggregate expression across cells in a SummarizedExperiment", "topics": [ "aggregateAcrossCells.se", "aggregateColData" ] }, { "page": "aggregateAcrossCellsDefaults", "title": "Default parameters for 'aggregateAcrossCells'", "topics": [ "aggregateAcrossCellsDefaults" ] }, { "page": "aggregateAcrossGenes", "title": "Aggregate expression across genes", "topics": [ "aggregateAcrossGenes" ] }, { "page": "aggregateAcrossGenes.se", "title": "Aggregate expression across gene sets in a SummarizedExperiment", "topics": [ "aggregateAcrossGenes.se" ] }, { "page": "aggregateAcrossGenesDefaults", "title": "Default parameters for 'aggregateAcrossGenes'", "topics": [ "aggregateAcrossGenesDefaults" ] }, { "page": "defunct", "title": "Defunct functions", "topics": [ "analyze", "convertAnalyzeResults" ] }, { "page": "analyze.se", "title": "Analyze single-cell data from a SummarizedExperiment", "topics": [ "analyze.se" ] }, { "page": "buildSnnGraph", "title": "Build a shared nearest neighbor graph", "topics": [ "buildSnnGraph" ] }, { "page": "buildSnnGraphDefaults", "title": "Default parameters for 'buildSnnGraph'", "topics": [ "buildSnnGraphDefaults" ] }, { "page": "centerSizeFactors", "title": "Center size factors", "topics": [ "centerSizeFactors" ] }, { "page": "centerSizeFactorsDefaults", "title": "Default parameters for 'centerSizeFactors'", "topics": [ "centerSizeFactorsDefaults" ] }, { "page": "centerSpikeInFactors", "title": "Center spike-in size factors", "topics": [ "centerSpikeInFactors" ] }, { "page": "centerSpikeInFactorsDefaults", "title": "Default parameters for 'centerSpikeInFactors'", "topics": [ "centerSpikeInFactorsDefaults" ] }, { "page": "chooseHighlyVariableGenes", "title": "Choose highly variable genes", "topics": [ "chooseHighlyVariableGenes" ] }, { "page": "chooseHighlyVariableGenesDefaults", "title": "Default parameters for 'chooseHighlyVariableGenes'", "topics": [ "chooseHighlyVariableGenesDefaults" ] }, { "page": "choosePseudoCount", "title": "Choose a suitable pseudo-count", "topics": [ "choosePseudoCount" ] }, { "page": "choosePseudoCountDefaults", "title": "Default parameters for 'choosePseudoCount'", "topics": [ "choosePseudoCountDefaults" ] }, { "page": "chooseRnaHvgs.se", "title": "Choose highly variable genes from a SummarizedExperiment", "topics": [ "chooseRnaHvgs.se", "formatModelGeneVariancesResult" ] }, { "page": "chooseRnaHvgsWithSpikeIns.se", "title": "Choose highly variable genes based on spike-ins", "topics": [ "chooseRnaHvgsWithSpikeIns.se" ] }, { "page": "clusterGraph", "title": "Graph-based clustering of cells", "topics": [ "clusterGraph" ] }, { "page": "clusterGraph.se", "title": "Graph-based clustering of cells in a SingleCellExperiment", "topics": [ "clusterGraph.se" ] }, { "page": "clusterGraphDefaults", "title": "Default parameters for 'clusterGraph'", "topics": [ "clusterGraphDefaults" ] }, { "page": "clusterKmeans", "title": "K-means clustering", "topics": [ "clusterKmeans" ] }, { "page": "clusterKmeans.se", "title": "k-means clustering of cells in a SingleCellExperiment", "topics": [ "clusterKmeans.se" ] }, { "page": "clusterKmeansDefaults", "title": "Default parameters for 'clusterKmeans'", "topics": [ "clusterKmeansDefaults" ] }, { "page": "combineFactors", "title": "Combine multiple factors", "topics": [ "combineFactors" ] }, { "page": "computeBlockWeights", "title": "Compute block weights", "topics": [ "computeBlockWeights" ] }, { "page": "computeBlockWeightsDefaults", "title": "Default parameters for 'computeBlockWeights'", "topics": [ "computeBlockWeightsDefaults" ] }, { "page": "computeClrm1Factors", "title": "Compute size factors for ADT counts", "topics": [ "computeClrm1Factors" ] }, { "page": "computeClrm1FactorsDefaults", "title": "Default parameters for 'computeClrm1Factors'", "topics": [ "computeClrm1FactorsDefaults" ] }, { "page": "correctMnn", "title": "Batch correction with mutual nearest neighbors", "topics": [ "correctMnn" ] }, { "page": "correctMnn.se", "title": "MNN correction on a SingleCellExperiment", "topics": [ "correctMnn.se" ] }, { "page": "correctMnnDefaults", "title": "Default parameters for 'correctMnn'", "topics": [ "correctMnnDefaults" ] }, { "page": "countGroupsByBlock", "title": "Count cells in groups and blocks", "topics": [ "countGroupsByBlock" ] }, { "page": "crispr_quality_control", "title": "Quality control for CRISPR count data", "topics": [ "computeCrisprQcMetrics", "crispr_quality_control", "filterCrisprQcMetrics", "suggestCrisprQcThresholds" ] }, { "page": "crispr_quality_control_defaults", "title": "Default parameters for CRISPR quality control", "topics": [ "computeCrisprQcMetricsDefaults", "crispr_quality_control_defaults", "suggestCrisprQcThresholdsDefaults" ] }, { "page": "fitVarianceTrend", "title": "Fit a mean-variance trend", "topics": [ "fitVarianceTrend" ] }, { "page": "fitVarianceTrendDefaults", "title": "Default parameters for 'fitVarianceTrend'", "topics": [ "fitVarianceTrendDefaults" ] }, { "page": "getTestData.se", "title": "Get datasets for testing", "topics": [ "getTestAdtData.se", "getTestCrisprData.se", "getTestData.se", "getTestRnaData.se" ] }, { "page": "LogNormalizedMatrix", "title": "Delayed log-normalization of a matrix", "topics": [ "DelayedArray,LogNormalizedMatrixSeed-method", "dim,LogNormalizedMatrixSeed-method", "dimnames,LogNormalizedMatrixSeed-method", "extract_array,LogNormalizedMatrixSeed-method", "extract_sparse_array,LogNormalizedMatrixSeed-method", "initializeCpp,LogNormalizedMatrixSeed-method", "is_sparse,LogNormalizedMatrixSeed-method", "LogNormalizedMatrix", "LogNormalizedMatrix-class", "LogNormalizedMatrixSeed", "LogNormalizedMatrixSeed-class", "matrixClass,LogNormalizedMatrixSeed-method", "type,LogNormalizedMatrixSeed-method" ] }, { "page": "modelGeneVariances", "title": "Model per-gene variances in expression", "topics": [ "modelGeneVariances" ] }, { "page": "modelGeneVariancesDefaults", "title": "Default parameters for 'modelGeneVariances'", "topics": [ "modelGeneVariancesDefaults" ] }, { "page": "normalizeAdtCounts.se", "title": "Normalize ADT counts in a SummarizedExperiment", "topics": [ "normalizeAdtCounts.se" ] }, { "page": "normalizeCounts", "title": "Normalize the count matrix", "topics": [ "normalizeCounts" ] }, { "page": "normalizeCountsDefaults", "title": "Default parameters for 'normalizeCounts'", "topics": [ "normalizeCountsDefaults" ] }, { "page": "normalizeCrisprCounts.se", "title": "Normalize CRISPR counts in a SummarizedExperiment", "topics": [ "normalizeCrisprCounts.se" ] }, { "page": "normalizeRnaCounts.se", "title": "Normalize RNA counts in a SummarizedExperiment", "topics": [ "normalizeRnaCounts.se" ] }, { "page": "normalizeRnaCountsWithSpikeIns.se", "title": "Normalize RNA and spike-in counts", "topics": [ "normalizeRnaCountsWithSpikeIns.se" ] }, { "page": "quickAdtQc.se", "title": "Quick quality control for ADT data in a SummarizedExperiment", "topics": [ "formatComputeAdtQcMetricsResult", "quickAdtQc.se" ] }, { "page": "quickCrisprQc.se", "title": "Quick quality control for CRISPR data in a SummarizedExperiment", "topics": [ "formatComputeCrisprQcMetricsResult", "quickCrisprQc.se" ] }, { "page": "quickRnaQc.se", "title": "Quick quality control for RNA data in a SummarizedExperiment", "topics": [ "computeRnaQcMetricsWithAltExps", "formatComputeRnaQcMetricsResult", "quickRnaQc.se" ] }, { "page": "reportGroupMarkerStatistics", "title": "Report marker statistics for a single group", "topics": [ "reportGroupMarkerStatistics" ] }, { "page": "rna_quality_control", "title": "Quality control for RNA count data", "topics": [ "computeRnaQcMetrics", "filterRnaQcMetrics", "rna_quality_control", "suggestRnaQcThresholds" ] }, { "page": "rna_quality_control_defaults", "title": "Default parameters for RNA quality control", "topics": [ "computeRnaQcMetricsDefaults", "rna_quality_control_defaults", "suggestRnaQcThresholdsDefaults" ] }, { "page": "runAllNeighborSteps", "title": "Run all neighbor-related steps", "topics": [ "runAllNeighborSteps" ] }, { "page": "runAllNeighborSteps.se", "title": "Run all nearest neighbor steps on a SummarizedExperiment", "topics": [ "runAllNeighborSteps.se" ] }, { "page": "runPca", "title": "Principal components analysis", "topics": [ "runPca" ] }, { "page": "runPca.se", "title": "Principal components analysis of a Summarizedexperiment", "topics": [ "runPca.se" ] }, { "page": "runPcaDefaults", "title": "Default parameters for 'runPca'", "topics": [ "runPcaDefaults" ] }, { "page": "runTsne", "title": "t-stochastic neighbor embedding", "topics": [ "runTsne", "tsnePerplexityToNeighbors" ] }, { "page": "runTsne.se", "title": "t-SNE on a SummarizedExperiment", "topics": [ "runTsne.se" ] }, { "page": "runTsneDefaults", "title": "Default parameters for 'runTsne'", "topics": [ "runTsneDefaults" ] }, { "page": "runUmap", "title": "Uniform manifold approximation and projection", "topics": [ "runUmap" ] }, { "page": "runUmap.se", "title": "UMAP on a SummarizedExperiment", "topics": [ "runUmap.se" ] }, { "page": "runUmapDefaults", "title": "Default parameters for 'runUmap'", "topics": [ "runUmapDefaults" ] }, { "page": "sanitizeSizeFactors", "title": "Sanitize size factors", "topics": [ "sanitizeSizeFactors" ] }, { "page": "sanitizeSizeFactorsDefaults", "title": "Default parameters for 'sanitizeSizeFactors'", "topics": [ "sanitizeSizeFactorsDefaults" ] }, { "page": "scaleByNeighbors", "title": "Scale and combine multiple embeddings", "topics": [ "scaleByNeighbors" ] }, { "page": "scaleByNeighbors.se", "title": "Scale and combine multiple embeddings in a SingleCellExperiment", "topics": [ "scaleByNeighbors.se" ] }, { "page": "scaleByNeighborsDefaults", "title": "Default parameters for 'scaleByNeighbors'", "topics": [ "scaleByNeighborsDefaults" ] }, { "page": "scoreGeneSet", "title": "Score gene set activity for each cell", "topics": [ "scoreGeneSet" ] }, { "page": "scoreGeneSet.se", "title": "Score a gene set in a SummarizedExperiment", "topics": [ "scoreGeneSet.se" ] }, { "page": "scoreGeneSetDefaults", "title": "Default parameters for 'scoreGeneSet'", "topics": [ "scoreGeneSetDefaults" ] }, { "page": "scoreMarkers", "title": "Score marker genes", "topics": [ "scoreMarkers" ] }, { "page": "scoreMarkers.se", "title": "Score marker genes in a SummarizedExperiment", "topics": [ "formatScoreMarkersResult", "previewMarkers", "scoreMarkers.se" ] }, { "page": "scoreMarkersDefaults", "title": "Default parameters for 'scoreMarkers'", "topics": [ "scoreMarkersDefaults" ] }, { "page": "subsampleByNeighbors", "title": "Subsample cells based on their neighbors", "topics": [ "subsampleByNeighbors" ] }, { "page": "subsampleByNeighborsDefaults", "title": "Default parameters for 'subsampleByNeighbors'", "topics": [ "subsampleByNeighborsDefaults" ] }, { "page": "subsampleByPartition", "title": "Subsample by partition", "topics": [ "subsampleByPartition" ] }, { "page": "subsampleByPartitionDefaults", "title": "Default parameters for 'subsampleByPartition'", "topics": [ "subsampleByPartitionDefaults" ] }, { "page": "summarizeEffects", "title": "Summarize pairwise effect sizes for each group", "topics": [ "summarizeEffects" ] }, { "page": "summarizeEffectsDefaults", "title": "Default parameters for 'summarizeEffectsDefaults'", "topics": [ "summarizeEffectsDefaults" ] }, { "page": "testEnrichment", "title": "Test for gene set enrichment", "topics": [ "testEnrichment" ] }, { "page": "testEnrichmentDefaults", "title": "Default parameters for 'testEnrichment'", "topics": [ "testEnrichmentDefaults" ] } ], "_readme": "https://github.com/bioc/scrapper/raw/HEAD/README.md", "_rundeps": [ "abind", "assorthead", "beachmat", "BiocGenerics", "biocmake", "BiocNeighbors", "DelayedArray", "dir.expiry", "filelock", "generics", "IRanges", "lattice", "Matrix", "MatrixGenerics", "matrixStats", "Rcpp", "Rigraphlib", "S4Arrays", "S4Vectors", "SparseArray", "XVector" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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": "userguide.Rmd", "filename": "userguide.html", "title": "Using scrapper to analyze single-cell data", "author": "Aaron Lun", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Basic analysis", "Blocking on batches", "Combining multiple modalities", "Other useful functions", "Session information" ], "created": "2024-09-08 23:25:44", "modified": "2025-12-26 02:51:17", "commits": 9 } ], "_score": 8.498119918720274, "_indexed": true, "_nocasepkg": "scrapper", "_universes": [ "bioc", "ltla", "libscran" ], "_binaries": [ { "r": "4.5.3", "os": "mac", "version": "1.5.17", "date": "2026-04-12T04:42:41.000Z", "arch": "aarch64", "commit": "b48a0663ab3fce3cf51130342d098c502b09e291", "fileid": "50b4a24425746e645df1ae608770eb95585ebcb14fe190b504a6e8b1c002476f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/24276220811" }, { "r": "4.5.3", "os": "mac", "version": "1.5.17", "date": "2026-04-12T04:44:53.000Z", "arch": "x86_64", "commit": "b48a0663ab3fce3cf51130342d098c502b09e291", "fileid": "686e9c1f2696c26df40a1c07eb2ee439759be9c228027fbfce01dd2c11a20cdf", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/24276220811" }, { "r": "4.6.0", "os": "mac", "version": "1.5.17", "date": "2026-04-12T04:46:50.000Z", "arch": "x86_64", "commit": "b48a0663ab3fce3cf51130342d098c502b09e291", "fileid": "8e97d6b4d24438894dd955f36b8268f2aaaa41b03a98fb7015e9279b5da71e66", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/24276220811" }, { "r": "4.7.0", "os": "linux", "version": "1.7.3", "date": "2026-05-19T11:19:01.000Z", "distro": "noble", "arch": "aarch64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "addc0164671b2a0a18b333465c9c0116065c4aadff2c83208995f95aa1627b41", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.7.0", "os": "linux", "version": "1.7.3", "date": "2026-05-19T11:19:32.000Z", "distro": "noble", "arch": "x86_64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "d543f4a992ee5d5a439299a514267bb4e2c46eaa29550c250874ee895f301e38", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.6.0", "os": "linux", "version": "1.7.3", "date": "2026-05-19T11:18:58.000Z", "distro": "noble", "arch": "aarch64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "2a4100e8783dbc02cfe274ee21ac9181d01a7e6d9582baf704e9bb243d6567e4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.6.0", "os": "linux", "version": "1.7.3", "date": "2026-05-19T11:20:30.000Z", "distro": "noble", "arch": "x86_64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "9071f031fe31dc080eb3a52ac55f18c825f4d7c022da0d1e0783485731cc3940", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.6.0", "os": "mac", "version": "1.7.3", "date": "2026-05-19T11:21:29.000Z", "arch": "aarch64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "f386bd3ac288b47fcf5b818563405a95696d1f6979416d731ae22f9add9af819", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.7.0", "os": "win", "version": "1.7.3", "date": "2026-05-19T11:34:23.000Z", "arch": "x86_64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "b86a0113cefad45d74f39066959983f03308ec2f964ca79aaa2c88a8d3a363b9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.5.3", "os": "win", "version": "1.7.3", "date": "2026-05-19T11:36:55.000Z", "arch": "x86_64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "8128ab2e059ed3c37f7b11c42a410dab106e2c5a14fd90a21dedbb9c998a405c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" }, { "r": "4.6.0", "os": "win", "version": "1.7.3", "date": "2026-05-19T11:37:31.000Z", "arch": "x86_64", "commit": "defe76d3933ce25103f33e82d79745398f63d912", "fileid": "eb14e05b996b12ae248ba901580f5fd8075e9e6f3209452436b1315047ae252e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26092903056" } ] }