{ "_id": "6a13f5b1acfb0bcc41d33162", "Package": "scaper", "Title": "Single Cell Transcriptomics-Level Cytokine Activity Prediction\nand Estimation", "Version": "0.2.1", "Authors@R": "c(\nperson(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\")),\nperson(\"H. Robert\", \"Frost\", email = \"hildreth.r.frost@dartmouth.edu\", role = c(\"aut\")),\nperson(\"Azka\", \"Javaid\", email = \"azka.javaid.gr@dartmouth.edu\", role = c(\"aut\")))", "Maintainer": "Zaoqu Liu ", "URL": "https://github.com/Zaoqu-Liu/scaper", "BugReports": "https://github.com/Zaoqu-Liu/scaper/issues", "Description": "Generates cell-level cytokine activity estimates using\nrelevant information from gene sets constructed with the\n'CytoSig' and the 'Reactome' databases and scored using the\nmodified 'Variance-adjusted Mahalanobis (VAM)' framework for\nsingle-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database\nis described in: Jiang at al., (2021)\n. 'Reactome' database is\ndescribed in: Gillespie et al., (2021)\n. The 'VAM' method is outlined in:\nFrost (2020) .", "License": "GPL (>= 2)", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 07:04:04 UTC", "User": "root" }, "Author": "Zaoqu Liu [aut, cre], H. Robert Frost [aut], Azka Javaid [aut]", "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": "2026-01-25 17:24:59 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/scaper", "RemoteRef": "main", "RemoteSha": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "MD5sum": "79fd838eab3a99437eb34d072b9f5caf", "_user": "zaoqu-liu", "_type": "src", "_file": "scaper_0.2.1.tar.gz", "_fileid": "bf7cc90733635da7787ac0b10d577111c8f84c4beaba7b6cdd7db4d1fa6b35ad", "_filesize": 670256, "_sha256": "bf7cc90733635da7787ac0b10d577111c8f84c4beaba7b6cdd7db4d1fa6b35ad", "_created": "2026-05-25T07:04:04.000Z", "_published": "2026-05-25T07:09:37.205Z", "_distro": "noble", "_jobs": [ { "job": 77670915010, "time": 238, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7193392387" }, { "job": 77670914971, "time": 247, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7193394187" }, { "job": 77670914989, "time": 116, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7193365899" }, { "job": 77670915028, "time": 118, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7193366345" }, { "job": 77670391635, "time": 275, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7193339342" }, { "job": 77670914978, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7193376870" }, { "job": 77670915025, "time": 181, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7193380168" }, { "job": 77670915023, "time": 281, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7193401722" }, { "job": 77670915100, "time": 215, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7193387961" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/scaper", "_commit": { "id": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "author": "Zaoqu-Liu ", "committer": "Zaoqu-Liu ", "message": "feat: 内置 VAM 算法，移除外部依赖\n\n- 新增 R/vam_internal.R: 内置 VAM 核心算法\n- 完全兼容 Seurat V4 和 V5\n- 移除对外部 VAM 包的依赖\n- 添加 MASS, Matrix, methods 作为依赖\n- 简化 vignettes 避免 R-universe 构建问题\n- 通过全部 21 项测试\n- R CMD check: 0 errors, 0 warnings, 0 notes\n", "time": 1769361899 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "magrittr", "role": "Imports" }, { "package": "xml2", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "SeuratObject", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" } ], "_owner": "zaoqu-liu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 6 } ], "_tags": [ { "name": "v0.2.1", "date": "2026-01-25" } ], "_stars": 0, "_contributors": [ { "user": "zaoqu-liu", "count": 6, "uuid": 68080738 } ], "_userbio": { "uuid": 68080738, "type": "user", "name": "LIU Zaoqu", "description": "AI4S" }, "_downloads": { "count": 564, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scaper" }, "_devurl": "https://github.com/zaoqu-liu/scaper", "_searchresults": 13, "_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/scaper.html", "manual.pdf" ], "_realowner": "cran", "_cranurl": false, "_releases": [ { "version": "0.1.0", "date": "2023-10-19" }, { "version": "0.2.0", "date": "2025-04-16" } ], "_exports": [ "%>%", "genesetCytoSig", "genesetReactome", "scape", "scapeForSeurat", "supportedCytokines" ], "_help": [ { "page": "genesetCytoSig", "title": "CytoSig gene set construction.", "topics": [ "genesetCytoSig" ] }, { "page": "genesetReactome", "title": "Reactome gene set construction.", "topics": [ "genesetReactome" ] }, { "page": "scape", "title": "Cytokine activity scores for a normalized matrix.", "topics": [ "scape" ] }, { "page": "scapeForSeurat", "title": "Cytokine activity scores for a Seurat matrix.", "topics": [ "scapeForSeurat" ] }, { "page": "supportedCytokines", "title": "Gene set to score for the CytoSig or the Reactome databases.", "topics": [ "supportedCytokines" ] } ], "_readme": "https://github.com/Zaoqu-Liu/scaper/raw/main/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "bitops", "bslib", "cachem", "caTools", "cli", "cluster", "codetools", "commonmark", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "deldir", "digest", "dotCall64", "dplyr", "dqrng", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "fs", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lmtest", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "progressr", "promises", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppTOML", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "Rtsne", "S7", "sass", "scales", "scattermore", "sctransform", "Seurat", "SeuratObject", "shiny", "sitmo", "sourcetools", "sp", "spam", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "survival", "sys", "tensor", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "uwot", "vctrs", "viridisLite", "withr", "xfun", "xml2", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "algorithm-details.Rmd", "filename": "algorithm-details.html", "title": "Algorithm Details: Mathematical Foundation of scaper", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Mathematical Formulation", "Variance-Adjusted Mahalanobis (VAM) Distance", "CDF Transformation", "Bidirectional Scoring (CytoSig)", "Gene Set Information", "CytoSig Database", "Weight Distribution", "Reactome Database", "Score Interpretation", "References", "Session Information" ], "created": "2026-01-25 06:41:26", "modified": "2026-01-25 17:24:59", "commits": 3 }, { "source": "introduction.Rmd", "filename": "introduction.html", "title": "Introduction to scaper: Cytokine Activity Estimation in Single Cells", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Key Features", "Installation", "Supported Cytokines", "CytoSig Database (n = 41)", "Reactome Database (n = 30)", "Quick Start", "Basic Usage with Seurat", "Basic Usage with Matrix", "Gene Set Construction", "CytoSig Gene Set Example", "Reactome Gene Set Example", "Score Interpretation", "Session Information" ], "created": "2026-01-25 06:41:26", "modified": "2026-01-25 17:24:59", "commits": 3 }, { "source": "scaper-vignette-CytoSig.Rmd", "filename": "scaper-vignette-CytoSig.html", "title": "Cytokine Activity Estimation using SCAPE (Single cell transcriptomics-level Cytokine Activity Prediction and Estimation): An Analysis using the CytoSig database.", "author": "Zaoqu Liu, Azka Javaid and H. Robert Frost", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-01-25 06:17:16", "modified": "2026-01-25 17:24:59", "commits": 2 }, { "source": "scaper-vignette-Reactome.Rmd", "filename": "scaper-vignette-Reactome.html", "title": "Cytokine Activity Estimation using SCAPE (Single cell transcriptomics-level Cytokine Activity Prediction and Estimation): An Analysis using the Reactome database.", "author": "Zaoqu Liu, Azka Javaid and H. Robert Frost", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-01-25 06:17:16", "modified": "2026-01-25 17:24:59", "commits": 2 }, { "source": "visualization.Rmd", "filename": "visualization.html", "title": "Visualization Guide for scaper", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Basic Heatmap", "Seurat Integration", "Distribution Analysis", "Correlation Analysis", "Best Practices", "Session Information" ], "created": "2026-01-25 06:41:26", "modified": "2026-01-25 17:24:59", "commits": 3 } ], "_score": 3.5118833609788744, "_indexed": false, "_nocasepkg": "scaper", "_universes": [ "zaoqu-liu" ], "_indexurl": "https://cran.r-universe.dev/scaper", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.2.1", "date": "2026-05-25T07:07:09.000Z", "distro": "noble", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "cbd32800c0129624297e2cef76ffe2abc702561d361a4953f1df8f33b5b359d7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.6.0", "os": "linux", "version": "0.2.1", "date": "2026-05-25T07:07:17.000Z", "distro": "noble", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "dbf3490562e248e347f11052268e741aefb9e74063fe16c02a3f749403397c5c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.5.3", "os": "mac", "version": "0.2.1", "date": "2026-05-25T07:05:44.000Z", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "09c91f3c0313890cf80ffd41dc5057f04e0c3e461a2d85d413c358b9ce2535e3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.6.0", "os": "mac", "version": "0.2.1", "date": "2026-05-25T07:05:44.000Z", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "f5ebfec3db065d703541c5b6b101d2d41117eb484e680b8813571d0f9e3dfb88", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.6.0", "os": "wasm", "version": "0.2.1", "date": "2026-05-25T07:07:18.000Z", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "3a5a0faf4984903be68520fda2d19b95554207815cb15122879a14cec91093c4", "status": "success", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.7.0", "os": "win", "version": "0.2.1", "date": "2026-05-25T07:06:03.000Z", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "c49edccc12bbb4abadb08fb525e820183cefb36c55f6d30bc1e655aea53c55c4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.5.3", "os": "win", "version": "0.2.1", "date": "2026-05-25T07:07:57.000Z", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "61c4c82bd1ce31a55253ae5e3de31992005dfeb5eed46dc3da1e4518c4fbc1b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" }, { "r": "4.6.0", "os": "win", "version": "0.2.1", "date": "2026-05-25T07:06:34.000Z", "commit": "76fae1d8a4f6e3ddeac379f47e608dcea3ade3a5", "fileid": "56c7c0921dc6bb43c41060e79dd4c3441ed94e9eb47f171b57749d4679e228ee", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26387859542" } ] }