{
  "_id": "6a2e3e5a3efcd9bda43057a4",
  "Package": "sciNOME",
  "Title": "Region-Centric Integration for Single-Cell Multi-Omics",
  "Version": "0.99.0",
  "Authors@R": "c(person(given = \"Shitao\",\nfamily = \"Zhou\",\nrole = c(\"aut\", \"cre\"),\nemail = \"m18231838586@163.com\",\ncomment = c(ORCID = \"0009-0005-0386-8870\")),\nperson(given = \"Medinfo\",\nfamily = \"Lab\",\nrole = \"fnd\"))",
  "Description": "Provides an end-to-end pipeline for processing RNA, DNA\nmethylation, and chromatin accessibility data at the\nsingle-cell level. It features ultra-fast data aggregation,\nquality control, dimensionality reduction, and multi-omics\nintegration based on genomic regions. Additionally, it offers\nextensive publication-ready visualization tools for downstream\nanalysis.",
  "License": "GPL-3",
  "URL": "https://github.com/Medinfo-Lab/sciNOME",
  "BugReports": "https://github.com/Medinfo-Lab/sciNOME/issues",
  "biocViews": "Software, SingleCell, Epigenetics, Transcriptomics,\nDNAMethylation, DifferentialExpression, DimensionReduction,\nClustering, QualityControl",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libxml2-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-06-14 04:00:54 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/sciNOME",
  "RemoteRef": "HEAD",
  "RemoteSha": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-14 05:33:30 UTC",
    "User": "root"
  },
  "Author": "Shitao Zhou [aut, cre] (ORCID: <https://orcid.org/0009-0005-0386-8870>),\nMedinfo Lab [fnd]",
  "Maintainer": "Shitao Zhou <m18231838586@163.com>",
  "MD5sum": "bc7ee57420e8ffa631c2f8a7b25664a7",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "sciNOME_0.99.0.tar.gz",
  "_fileid": "a0c3500b7e4134618e5aecc62d0857d5279ae297950a686c27163c67b3f9c7d0",
  "_filesize": 2940090,
  "_sha256": "a0c3500b7e4134618e5aecc62d0857d5279ae297950a686c27163c67b3f9c7d0",
  "_created": "2026-06-14T05:33:30.000Z",
  "_published": "2026-06-14T05:38:34.352Z",
  "_jobs": [
    {
      "job": 81252008741,
      "time": 188,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7617838959"
    },
    {
      "job": 81252008727,
      "time": 243,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7617845735"
    },
    {
      "job": 81252008730,
      "time": 257,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7617847381"
    },
    {
      "job": 81252008762,
      "time": 177,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7617837497"
    },
    {
      "job": 81252008746,
      "time": 171,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7617836921"
    },
    {
      "job": 81251713015,
      "time": 309,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7617816210"
    },
    {
      "job": 81252008733,
      "time": 168,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7617836648"
    },
    {
      "job": 81252008771,
      "time": 178,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7617837644"
    },
    {
      "job": 81252008764,
      "time": 196,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7617840609"
    },
    {
      "job": 81252008765,
      "time": 173,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7617837150"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 6
  },
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/BiocStaging/sciNOME",
  "_commit": {
    "id": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
    "author": "Medinfo Lad <m18231838586@163.com>",
    "committer": "Medinfo Lad <m18231838586@163.com>",
    "message": "Update DESCRIPTION\n",
    "time": 1781409654
  },
  "_maintainer": {
    "name": "Shitao Zhou",
    "email": "m18231838586@163.com",
    "login": "biubiubiu3322",
    "description": "",
    "uuid": 64774885
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.2.0",
      "role": "Depends"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "FNN",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "ggpubr",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "ggridges",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "impute",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "irlba",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "NMF",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "patchwork",
      "role": "Imports"
    },
    {
      "package": "pbapply",
      "role": "Imports"
    },
    {
      "package": "princurve",
      "role": "Imports"
    },
    {
      "package": "Rtsne",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "tidyselect",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "uwot",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-41",
      "n": 3
    },
    {
      "week": "2025-46",
      "n": 1
    },
    {
      "week": "2025-52",
      "n": 7
    },
    {
      "week": "2026-01",
      "n": 1
    },
    {
      "week": "2026-02",
      "n": 6
    },
    {
      "week": "2026-03",
      "n": 10
    },
    {
      "week": "2026-04",
      "n": 5
    },
    {
      "week": "2026-05",
      "n": 10
    },
    {
      "week": "2026-20",
      "n": 16
    },
    {
      "week": "2026-21",
      "n": 5
    },
    {
      "week": "2026-24",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "software",
    "singlecell",
    "epigenetics",
    "transcriptomics",
    "dnamethylation",
    "differentialexpression",
    "dimensionreduction",
    "clustering",
    "qualitycontrol"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "biubiubiu3322",
      "count": 64,
      "uuid": 64774885
    },
    {
      "user": "medinfo-lab",
      "count": 2,
      "uuid": 211216420
    }
  ],
  "_userbio": {
    "uuid": 278472782,
    "type": "organization",
    "name": "BiocStaging",
    "followers": 0
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/sciNOME"
  },
  "_devurl": "https://github.com/medinfo-lab/scinome",
  "_searchresults": 0,
  "_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/sciNOME.html",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "AddMetaData_RNA",
    "Aggregate_epiRegions",
    "Build_RNAObject",
    "CreateRNAObject",
    "Extract_epiData",
    "Integrate_MultiOmics",
    "PlotDimRed_Epi",
    "PlotDimRed_RNA",
    "PlotLandscape_Epi",
    "PlotOmicsMatrix",
    "PlotOmicsScatter",
    "PlotPseudo_RNA",
    "PlotQC_RNA",
    "PlotVolcano_Epi",
    "PlotVolcano_RNA",
    "ProcessQC_RNA",
    "QC_epiData",
    "Reduce_epiDims",
    "Run_Diffanalysis",
    "RunClustering_RNA",
    "RunDEA_RNA",
    "RunDimReduction_RNA",
    "RunPseudotime_RNA"
  ],
  "_help": [
    {
      "page": "AddMetaData_RNA",
      "title": "Add Metadata to a RNA Object",
      "topics": [
        "AddMetaData_RNA"
      ]
    },
    {
      "page": "Aggregate_epiRegions",
      "title": "Aggregate Bismark Coverage Files into Defined Genomic Regions",
      "topics": [
        "Aggregate_epiRegions"
      ]
    },
    {
      "page": "Build_RNAObject",
      "title": "Build a Complete RNA Object",
      "topics": [
        "Build_RNAObject"
      ]
    },
    {
      "page": "CreateRNAObject",
      "title": "Create a Lightweight RNA Object",
      "topics": [
        "CreateRNAObject"
      ]
    },
    {
      "page": "Extract_epiData",
      "title": "Extract Specific Metric Matrix from Aggregated Epigenetic Data",
      "topics": [
        "Extract_epiData"
      ]
    },
    {
      "page": "Integrate_MultiOmics",
      "title": "Integrate RNA, DNA Methylation (CpG), and Chromatin Accessibility (GpC) Data",
      "topics": [
        "Integrate_MultiOmics"
      ]
    },
    {
      "page": "PlotDimRed_Epi",
      "title": "Plot Dimensionality Reduction Results",
      "topics": [
        "PlotDimRed_Epi"
      ]
    },
    {
      "page": "PlotDimRed_RNA",
      "title": "Plot Dimensionality Reduction (PCA, t-SNE, UMAP)",
      "topics": [
        "PlotDimRed_RNA"
      ]
    },
    {
      "page": "PlotLandscape_Epi",
      "title": "Plot Epigenetic Landscape (Ridge Plot) from Level Matrix",
      "topics": [
        "PlotLandscape_Epi"
      ]
    },
    {
      "page": "PlotOmicsMatrix",
      "title": "Plot Multi-Omics Correlation Matrix",
      "topics": [
        "PlotOmicsMatrix"
      ]
    },
    {
      "page": "PlotOmicsScatter",
      "title": "Plot Multi-Omics Pairwise Scatter Plots",
      "topics": [
        "PlotOmicsScatter"
      ]
    },
    {
      "page": "PlotPseudo_RNA",
      "title": "Plot Trajectory and Pseudotime Inference",
      "topics": [
        "PlotPseudo_RNA"
      ]
    },
    {
      "page": "PlotQC_RNA",
      "title": "Plot Quality Control Metrics",
      "topics": [
        "PlotQC_RNA"
      ]
    },
    {
      "page": "PlotVolcano_Epi",
      "title": "Plot Volcano Plot for Differential Epigenetic Analysis",
      "topics": [
        "PlotVolcano_Epi"
      ]
    },
    {
      "page": "PlotVolcano_RNA",
      "title": "Plot Volcano Plot for Differential Expression Analysis",
      "topics": [
        "PlotVolcano_RNA"
      ]
    },
    {
      "page": "ProcessQC_RNA",
      "title": "Process QC, Filtering, and Normalization for RNA Object",
      "topics": [
        "ProcessQC_RNA"
      ]
    },
    {
      "page": "QC_epiData",
      "title": "Two-Step Quality Control for Epigenetic Matrix",
      "topics": [
        "QC_epiData"
      ]
    },
    {
      "page": "Reduce_epiDims",
      "title": "Run Dimensionality Reduction on Epigenetic Level Data",
      "topics": [
        "Reduce_epiDims"
      ]
    },
    {
      "page": "Run_Diffanalysis",
      "title": "Core Algorithm for Epigenetic Differential Region Analysis",
      "topics": [
        "Run_Diffanalysis"
      ]
    },
    {
      "page": "RunClustering_RNA",
      "title": "Run Clustering for RNA Object",
      "topics": [
        "RunClustering_RNA"
      ]
    },
    {
      "page": "RunDEA_RNA",
      "title": "Run Differential Expression Analysis (Wilcoxon Rank Sum Test)",
      "topics": [
        "RunDEA_RNA"
      ]
    },
    {
      "page": "RunDimReduction_RNA",
      "title": "Run Dimensionality Reduction (PCA, t-SNE, UMAP)",
      "topics": [
        "RunDimReduction_RNA"
      ]
    },
    {
      "page": "RunPseudotime_RNA",
      "title": "Run Pseudotime and Trajectory Inference",
      "topics": [
        "RunPseudotime_RNA"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/sciNOME/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "boot",
    "broom",
    "car",
    "carData",
    "cli",
    "cluster",
    "codetools",
    "colorspace",
    "corrplot",
    "cowplot",
    "cpp11",
    "data.table",
    "Deriv",
    "digest",
    "doBy",
    "doParallel",
    "dplyr",
    "dqrng",
    "farver",
    "FNN",
    "foreach",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggpubr",
    "ggrepel",
    "ggridges",
    "ggsci",
    "ggsignif",
    "glue",
    "gridBase",
    "gridExtra",
    "gtable",
    "igraph",
    "impute",
    "IRanges",
    "irlba",
    "isoband",
    "iterators",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "nlme",
    "nloptr",
    "NMF",
    "nnet",
    "numDeriv",
    "patchwork",
    "pbapply",
    "pbkrtest",
    "pillar",
    "pkgconfig",
    "plyr",
    "polynom",
    "princurve",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppAnnoy",
    "RcppArmadillo",
    "RcppEigen",
    "RcppProgress",
    "Rdpack",
    "reformulas",
    "registry",
    "reshape2",
    "rlang",
    "rngtools",
    "RSpectra",
    "rstatix",
    "Rtsne",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "sitmo",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "urca",
    "utf8",
    "uwot",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "Epi_Analysis.Rmd",
      "filename": "Epi_Analysis.html",
      "title": "Epigenetic Data Processing and Analysis using sciNOME",
      "author": "Shitao Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Setup and Mock Data Generation",
        "2. Data Aggregation",
        "3. Extracting specific Metrics and Quality Control",
        "4. Dimensionality Reduction",
        "5. Differential Epigenetic Analysis",
        "Session Information"
      ],
      "created": "2026-05-13 12:48:44",
      "modified": "2026-05-14 05:25:50",
      "commits": 2
    },
    {
      "source": "MultiOmics_Integration.Rmd",
      "filename": "MultiOmics_Integration.html",
      "title": "Multi-Omics Integration in sciNOME",
      "author": "Shitao Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Prepare Mock Multi-Omics Data",
        "1.1 Global Metadata",
        "1.2 Region Dictionary",
        "1.3 Simulate Omics Matrices",
        "2. Multi-Omics Integration",
        "Mode A: Tri-Omics Integration (RNA + CpG + GpC)",
        "Mode B: Dual Integration (RNA + CpG)",
        "Mode C: Epigenetics Only Integration (CpG + GpC)",
        "Session Information"
      ],
      "created": "2026-05-13 12:48:44",
      "modified": "2026-05-14 05:36:33",
      "commits": 3
    },
    {
      "source": "RNA_Analysis.Rmd",
      "filename": "RNA_Analysis.html",
      "title": "Single-Cell RNA Analysis Pipeline in sciNOME",
      "author": "Shitao Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Data Preparation",
        "2. Object Construction and QC",
        "3. Dimensionality Reduction",
        "4. Unsupervised Clustering",
        "5. Differential Expression Analysis (DEA)",
        "6. Trajectory Inference (Pseudotime)",
        "Session Information"
      ],
      "created": "2026-05-13 12:48:44",
      "modified": "2026-05-14 05:25:50",
      "commits": 2
    },
    {
      "source": "Plot.Rmd",
      "filename": "Plot.html",
      "title": "Visualization Gallery in sciNOME",
      "author": "Shitao Zhou",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "1. Single-Cell RNA Visualization",
        "1.1 Quality Control Plot",
        "1.2 Dimensionality Reduction Plot",
        "1.3 Volcano Plot for DEA",
        "1.4 Trajectory & Pseudotime Plot",
        "2. Epigenetic Visualization",
        "2.1 Epigenetic Landscape (Ridge Plot)",
        "2.2 Dimensionality Reduction for Epigenetics",
        "2.3 Epigenetic Volcano Plot",
        "3. Multi-Omics Integration Plots",
        "3.1 Omics Correlation Matrix",
        "3.2 Pairwise Scatter Plots",
        "Session Information"
      ],
      "created": "2026-05-14 05:25:50",
      "modified": "2026-05-14 05:36:33",
      "commits": 2
    }
  ],
  "_score": 4.342422680822207,
  "_indexed": true,
  "_nocasepkg": "scinome",
  "_universes": [
    "biocstaging",
    "biubiubiu3322",
    "medinfo-lab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-06-14T05:36:32.000Z",
      "distro": "noble",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "4769a848e21e8f96a9c594e54c43308f44c7dd62b2497e0af13a0931bff8aeef",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.0",
      "date": "2026-06-14T05:36:45.000Z",
      "distro": "noble",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "1d991c04f25493df53d1823f11ae551c2ab1b1f39dc364a6d429758005f7c3c5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-06-14T05:35:39.000Z",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "2586ae6dd5966780ebea16fc4d6d451e3bd83bbdf80f2b6a7c964eb07f34ed6a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.0",
      "date": "2026-06-14T05:35:41.000Z",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "670cade243b210b7dc5d6118269a217ea0bd40b6ba20d733e6ca3552c8f7e5a2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.0",
      "date": "2026-06-14T05:36:46.000Z",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "50d87fccb4cccbf9fee25ba5dfb590ade28e61b71eb1ca9c829a5f3a5a7983ab",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-06-14T05:35:25.000Z",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "0369c93164797dd2f3bc147de5bad138955840b15c933ba104b9b2c67a706c1e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-06-14T05:35:44.000Z",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "8bce7cb0fa44df2dde8e8e720b3928d260eae49174b48dbc530c23ef73c8576f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.99.0",
      "date": "2026-06-14T05:35:14.000Z",
      "commit": "890d8da44f95cacec589dd82a9b6f3e4e85b51ca",
      "fileid": "a524db1eaf053f324a68977992baf3ca35f66fd9fb79db8956620c084a534a64",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/27489461904"
    }
  ]
}