{ "_id": "6a1d4e561d7bb097a0a446cc", "Package": "CytoSPACER", "Type": "Package", "Title": "Mapping Single-Cell Transcriptomes to Spatial Transcriptomics\nData", "Version": "1.0.0", "Date": "2026-01-25", "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\",\nemail = \"liuzaoqu@163.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-5623-6869\")),\nperson(\"CytoSPACE Team\", role = \"ctb\",\ncomment = \"Original Python implementation\"))", "Description": "CytoSPACER is an R implementation of CytoSPACE, a\ncomputational strategy for assigning single-cell transcriptomes\nto in situ spatial transcriptomics (ST) data. The method solves\nsingle cell/spot assignment by minimizing a correlation-based\ncost function through a linear programming-based optimization\nroutine using the Jonker-Volgenant algorithm. This package\nprovides high-performance implementations using Rcpp and\nsupports parallel processing across all platforms.", "License": "MIT + file LICENSE", "URL": "https://zaoqu-liu.github.io/CytoSPACER/,\nhttps://github.com/Zaoqu-Liu/CytoSPACER", "BugReports": "https://github.com/Zaoqu-Liu/CytoSPACER/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-24 18:51:37 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/CytoSPACER", "RemoteRef": "main", "RemoteSha": "885560a47a2170304bac1c921277a4633ee7a2e0", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 09:10:16 UTC", "User": "root" }, "Author": "Zaoqu Liu [aut, cre] (ORCID: ),\nCytoSPACE Team [ctb] (Original Python implementation)", "Maintainer": "Zaoqu Liu ", "MD5sum": "a26d375e6e9028b287a7086e41989dcc", "_user": "zaoqu-liu", "_type": "src", "_file": "CytoSPACER_1.0.0.tar.gz", "_fileid": "4a29d6885449ad4d9c6011f8615a3cd1fef75d720cdee7e8b71c7e7f335dc1ff", "_filesize": 1045169, "_sha256": "4a29d6885449ad4d9c6011f8615a3cd1fef75d720cdee7e8b71c7e7f335dc1ff", "_created": "2026-06-01T09:10:16.000Z", "_published": "2026-06-01T09:18:14.761Z", "_distro": "noble", "_jobs": [ { "job": 78820888982, "time": 201, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7327654561" }, { "job": 78820888992, "time": 190, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7327651331" }, { "job": 78820889064, "time": 213, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7327658526" }, { "job": 78820888990, "time": 234, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7327665549" }, { "job": 78820889048, "time": 169, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7327644121" }, { "job": 78820888979, "time": 326, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7327694855" }, { "job": 78820889077, "time": 119, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7327626407" }, { "job": 78820888928, "time": 423, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7327729270" }, { "job": 78820178290, "time": 268, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7327585417" }, { "job": 78820888882, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7327641591" }, { "job": 78820888978, "time": 175, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7327646339" }, { "job": 78820888913, "time": 188, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7327650538" }, { "job": 78820888931, "time": 182, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7327648696" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/CytoSPACER", "_commit": { "id": "885560a47a2170304bac1c921277a4633ee7a2e0", "author": "Zaoqu-Liu ", "committer": "Zaoqu-Liu ", "message": "Complete Python parity: sampling_sub_spots mode, -correlation cost, comprehensive tests\n\n- Implemented sampling_sub_spots mode for large datasets (exact Python behavior)\n- Implemented single_cell mode with typed/untyped variants\n- Changed cost calculation from (1-correlation) to (-correlation) to match Python\n- Added number_of_selected_spots and number_of_selected_sub_spots parameters\n- Added parallel processing support with n_workers parameter\n- Updated all tests to reflect new cost calculation range [-1,1]\n- Added comprehensive test suite for all run_cytospace modes\n- All 194 tests passing, R CMD check 0 errors 0 warnings\n", "time": 1769280697 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "orcid": "0000-0002-5623-6869", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.10", "role": "Imports" }, { "package": "data.table", "version": ">= 1.14.0", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.5.0", "role": "Imports" }, { "package": "future", "version": ">= 1.32.0", "role": "Imports" }, { "package": "future.apply", "version": ">= 1.11.0", "role": "Imports" }, { "package": "progressr", "version": ">= 0.14.0", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.0.0", "role": "Suggests" }, { "package": "SeuratObject", "version": ">= 4.0.0", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" } ], "_owner": "zaoqu-liu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 8 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "zaoqu-liu", "count": 8, "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/CytoSPACER" }, "_devurl": "https://github.com/zaoqu-liu/cytospacer", "_pkgdown": "https://zaoqu-liu.github.io/CytoSPACER/", "_searchresults": 7, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/CytoSPACER.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "add_cytospace_to_seurat", "add_noise_to_cost", "compute_assignment_cost", "compute_cost_matrix", "downsample_expression", "estimate_cell_type_fractions", "estimate_cells_per_spot", "estimate_fractions", "extract_seurat_data", "extract_spatial_data", "normalize_expression", "plot_composition", "plot_cytospace", "read_cytospace_input", "read_visium_data", "run_cytospace", "run_cytospace_seurat", "sample_cells", "sample_cells_by_type", "save_cytospace_plot", "solve_lap", "solve_lap_parallel", "write_cytospace_results" ], "_help": [ { "page": "add_cytospace_to_seurat", "title": "Add CytoSPACER Results to Seurat Object", "topics": [ "add_cytospace_to_seurat" ] }, { "page": "add_noise_to_cost", "title": "Add Noise to Cost Matrix", "topics": [ "add_noise_to_cost" ] }, { "page": "cell_sampling", "title": "Cell Sampling Functions for CytoSPACER", "topics": [ "cell_sampling" ] }, { "page": "compute_assignment_cost", "title": "Compute Total Assignment Cost", "topics": [ "compute_assignment_cost" ] }, { "page": "compute_cost_matrix", "title": "Compute Cost Matrix", "topics": [ "compute_cost_matrix" ] }, { "page": "cost_matrix", "title": "Cost Matrix Computation for CytoSPACER", "topics": [ "cost_matrix" ] }, { "page": "data_io", "title": "Data Input/Output Functions for CytoSPACER", "topics": [ "data_io" ] }, { "page": "downsample_expression", "title": "Downsample Expression Matrix", "topics": [ "downsample_expression" ] }, { "page": "estimate_cells_per_spot", "title": "Estimate Cells per Spot", "topics": [ "estimate_cells_per_spot" ] }, { "page": "estimate_fractions", "title": "Estimate Cell Type Fractions", "topics": [ "estimate_cell_type_fractions", "estimate_fractions" ] }, { "page": "extract_seurat_data", "title": "Extract CytoSPACER Input from Seurat Object", "topics": [ "extract_seurat_data" ] }, { "page": "extract_spatial_data", "title": "Extract Spatial Data from Seurat Object", "topics": [ "extract_spatial_data" ] }, { "page": "lap_solver", "title": "Linear Assignment Problem Solvers for CytoSPACER", "topics": [ "lap_solver" ] }, { "page": "main", "title": "Main CytoSPACER Analysis Functions", "topics": [ "main" ] }, { "page": "normalization", "title": "Data Normalization Functions for CytoSPACER", "topics": [ "normalization" ] }, { "page": "normalize_expression", "title": "Normalize Expression Data", "topics": [ "normalize_expression" ] }, { "page": "plot_composition", "title": "Plot Cell Type Composition", "topics": [ "plot_composition" ] }, { "page": "plot_cytospace", "title": "Plot CytoSPACER Results", "topics": [ "plot_cytospace" ] }, { "page": "plotting", "title": "Visualization Functions for CytoSPACER", "topics": [ "plotting" ] }, { "page": "read_cytospace_input", "title": "Read CytoSPACER Input Files", "topics": [ "read_cytospace_input" ] }, { "page": "read_visium_data", "title": "Read Visium Data from SpaceRanger Output", "topics": [ "read_visium_data" ] }, { "page": "run_cytospace", "title": "Run CytoSPACE Analysis", "topics": [ "run_cytospace" ] }, { "page": "run_cytospace_seurat", "title": "Run CytoSPACER from Seurat Objects", "topics": [ "run_cytospace_seurat" ] }, { "page": "sample_cells", "title": "Sample Single Cells by Cell Type Composition", "topics": [ "sample_cells", "sample_cells_by_type" ] }, { "page": "save_cytospace_plot", "title": "Save CytoSPACER Plots", "topics": [ "save_cytospace_plot" ] }, { "page": "seurat_integration", "title": "Seurat Integration Functions for CytoSPACER", "topics": [ "seurat_integration" ] }, { "page": "solve_lap", "title": "Solve Linear Assignment Problem", "topics": [ "solve_lap" ] }, { "page": "solve_lap_parallel", "title": "Solve Multiple Assignment Problems in Parallel", "topics": [ "solve_lap_parallel" ] }, { "page": "utils", "title": "Utility Functions for CytoSPACER", "topics": [ "utils" ] }, { "page": "write_cytospace_results", "title": "Write CytoSPACER Results", "topics": [ "write_cytospace_results" ] } ], "_readme": "https://github.com/Zaoqu-Liu/CytoSPACER/raw/main/README.md", "_rundeps": [ "cli", "codetools", "cpp11", "data.table", "digest", "farver", "future", "future.apply", "ggplot2", "globals", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "listenv", "Matrix", "parallelly", "progressr", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "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": "algorithm.Rmd", "filename": "algorithm.html", "title": "Algorithm Principles", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Overview", "The Spatial Mapping Problem", "Problem Statement", "Mathematical Formulation", "Algorithm Pipeline", "Step 1: Cell Type Fraction Estimation", "Step 2: Cell Count Estimation", "Step 3: Reference Cell Sampling", "Step 4: Cost Matrix Construction", "Step 5: Linear Assignment Problem Solving", "The Jonker-Volgenant Algorithm", "Implementation Details", "Distance Metrics", "Pearson Correlation", "Spearman Correlation", "Euclidean Distance", "Normalization", "Handling Large Datasets", "Tie-Breaking", "References", "Session Info" ], "created": "2026-01-24 18:29:19", "modified": "2026-01-24 18:29:19", "commits": 1 }, { "source": "performance.Rmd", "filename": "performance.html", "title": "Performance Optimization", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Performance Architecture", "Benchmarking", "C++ vs R Implementation", "LAP Solver Performance", "Memory Optimization", "Sparse Matrix Handling", "Downsampling", "Parallel Processing", "Setting Up Workers", "Parallel LAP Solving", "Using Future Plans", "Chunked Processing", "How Chunking Works", "Optimization Guidelines", "Dataset Size Recommendations", "Memory Guidelines", "Best Practices", "Profiling", "Time Profiling", "Troubleshooting Performance Issues", "Issue: Out of Memory", "Issue: Slow Performance", "Session Info" ], "created": "2026-01-24 18:29:19", "modified": "2026-01-24 18:29:19", "commits": 1 }, { "source": "quick-start.Rmd", "filename": "quick-start.html", "title": "Quick Start Guide", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Load the Package", "Simulated Example", "Run CytoSPACER", "Explore Results", "Visualization", "Spatial Cell Type Distribution", "With Jitter for Dense Regions", "Cell Type Composition", "Summary Statistics", "Save Results", "Next Steps", "Session Info" ], "created": "2026-01-24 18:29:19", "modified": "2026-01-24 18:29:19", "commits": 1 }, { "source": "seurat-integration.Rmd", "filename": "seurat-integration.html", "title": "Seurat Integration", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Prerequisites", "Workflow Overview", "Loading Data", "From Seurat Objects", "From 10x Visium Output", "Running CytoSPACER with Seurat", "Direct Analysis", "Using Idents", "Adding Results to Seurat", "Basic Integration", "Visualizing with Seurat", "Data Extraction Utilities", "Extract scRNA-seq Data", "Extract Spatial Data", "Save to Files", "Complete Workflow Example", "Working with Seurat v5", "Tips and Best Practices", "1. Cell Type Annotation Quality", "2. Gene Overlap", "3. Memory Management", "Troubleshooting", "Common Issues", "Session Info" ], "created": "2026-01-24 18:29:19", "modified": "2026-01-24 18:29:19", "commits": 1 }, { "source": "visualization.Rmd", "filename": "visualization.html", "title": "Visualization Gallery", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup", "Generate Example Data", "Basic Spatial Plots", "Cell Type Distribution", "Customizing Point Size and Transparency", "Adding Jitter", "Custom Colors", "Custom Title", "Cell Type Composition Plots", "Global Composition", "With Custom Colors", "Advanced Visualizations", "Combining with ggplot2", "Faceted by Cell Type", "Saving Plots", "Color Palettes", "Session Info" ], "created": "2026-01-24 18:29:19", "modified": "2026-01-24 18:29:19", "commits": 1 } ], "_score": 3.3979400086720375, "_indexed": true, "_nocasepkg": "cytospacer", "_universes": [ "zaoqu-liu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-01T09:13:12.000Z", "distro": "noble", "arch": "aarch64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "8796c7f3a4806f3007b4a569ed42ae0b5fa9a86a0052d801a70189e0b3ce3eed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-06-01T09:12:57.000Z", "distro": "noble", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "6c469a41f3786731f6f1c5899fa135010c404f0171c3d7b8dfcaa20c4a555763", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-01T09:13:24.000Z", "distro": "noble", "arch": "aarch64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "eaad92fb9e82ba4f3ff33c1e634cb7adbf7faf7195ec6f10fc8c738e1a10caa2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-06-01T09:13:38.000Z", "distro": "noble", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "e25b60ebb8998633ee323b326e7384b20c5ea48f66c9b9fe3bf8cb735ec9dd10", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-01T09:12:38.000Z", "arch": "aarch64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "407b1d3d3d30a4d59f0c9abd01c4558525cc4f8b8003af07c8a36ace290f6451", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-06-01T09:13:57.000Z", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "9d90f8c2b88ee0a22a24c7a78bf35f9a4e890496f1b4bc2d2c6f1dd15041c1c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-01T09:12:04.000Z", "arch": "aarch64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "a3eaa54e928c236bc5f56f4c725b4a610f6c74d7082c4effd842efa17cd1b4a7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-06-01T09:15:37.000Z", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "cbf6a742805136566d84d63cbf10696aad06de546b948b092703080df84ce041", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-06-01T09:13:17.000Z", "arch": "emscripten", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "c1518049853b0a831cce63201d5c65f180ed14e4ffa2dfbffdb09f81c866bc96", "status": "success", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-06-01T09:12:13.000Z", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "4424eb10f08fddb55deca5e3cb4dbafb538149eda33c72b6bf37d0fd2183f9df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-06-01T09:12:19.000Z", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "bb612ae4cd41e979bdbb31ca0ebbd11351be2a9744d3b89e74df44f52591b721", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-06-01T09:12:16.000Z", "arch": "x86_64", "commit": "885560a47a2170304bac1c921277a4633ee7a2e0", "fileid": "2b9d7fec8c653c054f0bc3f64ffe0694b45ca40ad1702e16d5c2da0297c30e85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26745586660" } ] }