{
  "_id": "6a149732acfb0bcc41d4969f",
  "Package": "symphony",
  "Title": "Efficient and Precise Single-Cell Reference Atlas Mapping",
  "Version": "0.1.3",
  "Authors@R": "c(\nperson(given = \"Joyce\", family = \"Kang\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-1962-1291\"),\nemail = \"joyce.b.kang@gmail.com\"),\nperson(\"Ilya\", \"Korsunsky\", email = \"ilya.korsunsky@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-4848-3948\")),\nperson(\"Soumya\", \"Raychaudhuri\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-1901-8265\"))\n)",
  "Description": "Implements the Symphony single-cell reference building and\nquery mapping algorithms and additional functions described in\nKang et al\n<https://www.nature.com/articles/s41467-021-25957-x>.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-25 18:32:20 UTC",
    "User": "root"
  },
  "Author": "Joyce Kang [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1962-1291>), Ilya Korsunsky [aut]\n(ORCID: <https://orcid.org/0000-0003-4848-3948>), Soumya\nRaychaudhuri [aut] (ORCID:\n<https://orcid.org/0000-0002-1901-8265>)",
  "Maintainer": "Joyce Kang <joyce.b.kang@gmail.com>",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://joycekang.r-universe.dev",
  "Date/Publication": "2026-05-25 15:20:02 UTC",
  "RemoteUrl": "https://github.com/cran/symphony",
  "RemoteRef": "HEAD",
  "RemoteSha": "1124a8c1e64f28327decfeec4483dbb763a9782f",
  "MD5sum": "b4b9779a955ed717e3ac4ca137b265c8",
  "_user": "joycekang",
  "_type": "src",
  "_file": "symphony_0.1.3.tar.gz",
  "_fileid": "3c8d604fec98f3f144e40173ef25c129359e8890cd2f9e128e63ba64b08e1f6b",
  "_filesize": 1058387,
  "_sha256": "3c8d604fec98f3f144e40173ef25c129359e8890cd2f9e128e63ba64b08e1f6b",
  "_created": "2026-05-25T18:32:20.000Z",
  "_published": "2026-05-25T18:38:42.030Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77756288093,
      "time": 200,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7203253735"
    },
    {
      "job": 77756288116,
      "time": 206,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7203255036"
    },
    {
      "job": 77756288120,
      "time": 203,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203254136"
    },
    {
      "job": 77756288115,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203250208"
    },
    {
      "job": 77756288154,
      "time": 132,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7203239686"
    },
    {
      "job": 77756288101,
      "time": 246,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7203263106"
    },
    {
      "job": 77756288105,
      "time": 120,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203236878"
    },
    {
      "job": 77756288104,
      "time": 326,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203278800"
    },
    {
      "job": 77755766262,
      "time": 287,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203211573"
    },
    {
      "job": 77756288083,
      "time": 145,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203242040"
    },
    {
      "job": 77756288089,
      "time": 152,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7203243648"
    },
    {
      "job": 77756288102,
      "time": 161,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7203245584"
    },
    {
      "job": 77756288125,
      "time": 171,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7203247833"
    }
  ],
  "_buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/symphony",
  "_commit": {
    "id": "1124a8c1e64f28327decfeec4483dbb763a9782f",
    "author": "Joyce Kang <joyce.b.kang@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 0.1.3\n",
    "time": 1779722402
  },
  "_maintainer": {
    "name": "Joyce Kang",
    "email": "joyce.b.kang@gmail.com",
    "login": "joycekang",
    "description": "",
    "uuid": 12923683,
    "orcid": "0000-0002-1962-1291"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "harmony",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "class",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "ggthemes",
      "role": "Suggests"
    },
    {
      "package": "ggrepel",
      "role": "Suggests"
    },
    {
      "package": "ggrastr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2026-22",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.1.2",
      "date": "2025-10-31"
    },
    {
      "name": "0.1.3",
      "date": "2026-05-25"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "joycekang",
      "count": 4,
      "uuid": 12923683
    }
  ],
  "_userbio": {
    "uuid": 12923683,
    "type": "user",
    "name": "Joyce Kang"
  },
  "_downloads": {
    "count": 480,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/symphony"
  },
  "_searchresults": 187,
  "_topics": [
    "openblas",
    "cpp"
  ],
  "_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/symphony.html",
    "manual.pdf"
  ],
  "_realowner": "joycekang",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2021-08-05"
    },
    {
      "version": "0.1.1",
      "date": "2023-01-16"
    },
    {
      "version": "0.1.2",
      "date": "2025-10-31"
    },
    {
      "version": "0.1.3",
      "date": "2026-05-25"
    }
  ],
  "_exports": [
    "buildReference",
    "buildReferenceFromHarmonyObj",
    "calcknncorr",
    "calcknncorrWithinQuery",
    "calcPerCellMappingMetric",
    "calcPerClusterMappingMetric",
    "evaluate",
    "findVariableGenes",
    "knnPredict",
    "mapQuery",
    "plotReference",
    "rowSDs",
    "runPCAQueryAlone",
    "scaleDataWithStats",
    "vargenes_vst"
  ],
  "_datasets": [
    {
      "name": "pbmcs_exprs_small",
      "title": "Log(CP10k+1) normalized counts matrix (genes by cells) for 10x PBMCs dataset for vignette.",
      "object": "pbmcs_exprs_small",
      "class": [
        "dgCMatrix"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "pbmcs_meta_small",
      "title": "Metadata for 10x PBMCs dataset for vignette.",
      "object": "pbmcs_meta_small",
      "class": [
        "data.frame"
      ],
      "fields": [
        "cell_id",
        "donor",
        "nUMI",
        "nGene",
        "percent_mito",
        "cell_type",
        "cell_type_broad"
      ],
      "rows": 1200,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "buildReference",
      "title": "Function for building a Symphony reference starting from expression matrix",
      "topics": [
        "buildReference"
      ]
    },
    {
      "page": "buildReferenceFromHarmonyObj",
      "title": "Function for building a Symphony reference from a Harmony object. Useful if you would like your code to be more modular. Note that you must have saved vargenes_means_sds and PCA loadings.",
      "topics": [
        "buildReferenceFromHarmonyObj"
      ]
    },
    {
      "page": "calcknncorr",
      "title": "Calculates the k-NN correlation, which measures how well the sorted ordering of k nearest reference neighbors in a gold standard embedding correlate with the ordering for the same reference cells in an alternative embedding (i.e. from reference mapping). NOTE: it is very important for the order of reference cells (cols) in gold_ref matches that of alt_ref (same for matching columns of gold_query and alt_query).",
      "topics": [
        "calcknncorr"
      ]
    },
    {
      "page": "calcknncorrWithinQuery",
      "title": "Calculates the k-NN correlation within the query cells only, which measures how well the sorted ordering of k nearest query neighbors in a query de novo PCA embedding correlate with the ordering for the cells in the reference mapping embedding.",
      "topics": [
        "calcknncorrWithinQuery"
      ]
    },
    {
      "page": "calcPerCellMappingMetric",
      "title": "Per-cell Confidence Score: Calculates the weighted Mahalanobis distance for the query cells to reference clusters. Returns a vector of distance scores, one per query cell. Higher distance metric indicates less confidence.",
      "topics": [
        "calcPerCellMappingMetric"
      ]
    },
    {
      "page": "calcPerClusterMappingMetric",
      "title": "Per-cluster Confidence Score: Calculates the Mahalanobis distance from user-defined query clusters to their nearest reference centroid after initial projection into reference PCA space. All query cells in a cluster get the same score. Higher distance indicates less confidence. Due to the instability of estimating covariance with small numbers of cells, we do not assign a score to clusters smaller than u * d, where d is the dimensionality of the embedding and u is specified.",
      "topics": [
        "calcPerClusterMappingMetric"
      ]
    },
    {
      "page": "evaluate",
      "title": "Function for evaluating F1 by cell type, adapted from automated cell type identifiaction benchmarking paper (Abdelaal et al. Genome Biology, 2019)",
      "topics": [
        "evaluate"
      ]
    },
    {
      "page": "findVariableGenes",
      "title": "Function to find variable genes using mean variance relationship method",
      "topics": [
        "findVariableGenes"
      ]
    },
    {
      "page": "knnPredict",
      "title": "Predict annotations of query cells from the reference using k-NN method",
      "topics": [
        "knnPredict"
      ]
    },
    {
      "page": "mapQuery",
      "title": "Function for mapping query cells to a Symphony reference",
      "topics": [
        "mapQuery"
      ]
    },
    {
      "page": "pbmcs_exprs_small",
      "title": "Log(CP10k+1) normalized counts matrix (genes by cells) for 10x PBMCs dataset for vignette.",
      "topics": [
        "pbmcs_exprs_small"
      ]
    },
    {
      "page": "pbmcs_meta_small",
      "title": "Metadata for 10x PBMCs dataset for vignette.",
      "topics": [
        "pbmcs_meta_small"
      ]
    },
    {
      "page": "plotReference",
      "title": "Function to plot reference, colored by cell type",
      "topics": [
        "plotReference"
      ]
    },
    {
      "page": "rowSDs",
      "title": "Calculate standard deviations by row",
      "topics": [
        "rowSDs"
      ]
    },
    {
      "page": "runPCAQueryAlone",
      "title": "Runs a standard PCA pipeline on query (1 batch). Assumes query_exp is already normalized.",
      "topics": [
        "runPCAQueryAlone"
      ]
    },
    {
      "page": "scaleDataWithStats",
      "title": "Scale data with given mean and standard deviations",
      "topics": [
        "scaleDataWithStats"
      ]
    },
    {
      "page": "vargenes_vst",
      "title": "Function to find variable genes using variance stabilizing transform (vst) method",
      "topics": [
        "vargenes_vst"
      ]
    }
  ],
  "_readme": "https://github.com/cran/symphony/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "class",
    "cli",
    "cowplot",
    "cpp11",
    "data.table",
    "dplyr",
    "dqrng",
    "farver",
    "FNN",
    "generics",
    "ggplot2",
    "glue",
    "gtable",
    "harmony",
    "irlba",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "RANN",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppProgress",
    "RhpcBLASctl",
    "rlang",
    "RSpectra",
    "S7",
    "scales",
    "sitmo",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_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": "quickstart_tutorial.Rmd",
      "filename": "quickstart_tutorial.html",
      "title": "Quickstart Tutorial",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Load the data",
        "Build Symphony reference",
        "Option 1: Build from Harmony object (preferred method)",
        "Option 2: Build from scratch (starting with expression)",
        "Map query",
        "Visualization of mapping"
      ],
      "created": "2021-08-05 06:50:05",
      "modified": "2026-05-25 15:20:02",
      "commits": 3
    }
  ],
  "_score": 4.2718416065364995,
  "_indexed": true,
  "_nocasepkg": "symphony",
  "_universes": [
    "joycekang"
  ],
  "_previous": "0.1.2",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.3",
      "date": "2026-05-25T18:35:27.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "de5c1c0053afd7bc718f1aaf3743016c415f8b2f54bdf98c3ea4cefad2ce3db3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.3",
      "date": "2026-05-25T18:35:30.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "bb5fc50e053f081d24f15c8b185a40cc3d3eae1fdc1e869a969c02454583a08c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.3",
      "date": "2026-05-25T18:35:30.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "76c54f80115fa4c52ef2825f56c1560d660f095dd94f9f624c2b1369610158cb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.3",
      "date": "2026-05-25T18:35:11.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "652a829763128c4b6a7a39accd822ec8eca03f5612074c6251e8badca6564c82",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.3",
      "date": "2026-05-25T18:34:33.000Z",
      "arch": "aarch64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "d57835e70f1b59d84fdca339f334c9f9260dd1790b4d2150fd7fe6f91bc209a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.3",
      "date": "2026-05-25T18:35:36.000Z",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "2d8d6c23316cd6b5fa77e71c62b2e48110ba1a2c89ffd5d650f7767f3bfaa76d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.3",
      "date": "2026-05-25T18:34:22.000Z",
      "arch": "aarch64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "08c7434fce47d97ad989b4789a604abb8ccd27ce95950b996a3f6f16e21d3081",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.3",
      "date": "2026-05-25T18:36:40.000Z",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "87a236da2faef5f1a62d2804f5f392710a5ec943a611c0fa4b819b42c2f3e5a4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.3",
      "date": "2026-05-25T18:35:11.000Z",
      "arch": "emscripten",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "fd6809957c2b3d96f529fe4f19cfb19bbe3f1bc195e54edcd9ecd102a0e390d4",
      "status": "success",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.3",
      "date": "2026-05-25T18:34:17.000Z",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "0065b42206ab51aefa4e579bc406fefee0e3c6739bda5f8b8ed7becf2584c06d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.3",
      "date": "2026-05-25T18:34:19.000Z",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "0fa69bed3aad79a5af1e61f492dc22197733c4cfaff50896d41b5e637c986888",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.3",
      "date": "2026-05-25T18:34:25.000Z",
      "arch": "x86_64",
      "commit": "1124a8c1e64f28327decfeec4483dbb763a9782f",
      "fileid": "eee8543cdc155c33e21d02bc38866fe2e21dc6db3d5b0c9a0ad0f2ae3b3c959d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/joycekang/actions/runs/26414446094"
    }
  ]
}