{
  "_id": "6a1023eaacfb0bcc41c8d955",
  "Package": "splikit",
  "Title": "Analysing RNA Splicing in Single-Cell RNA Sequencing Data",
  "Version": "2.3.1",
  "Authors@R": "person(\"Arsham\", \"Mikaeili Namini\", , \"arsham.mikaeilinamini@mail.mcgill.ca\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-9453-6951\"))",
  "Description": "Provides analysis of high-dimensional single-cell splicing\ndata. Offers a framework to extract and work with ratio-based\ndata structures derived from single-cell RNA sequencing\nexperiments. Provides both a modern 'R6' object-oriented\ninterface and direct matrix manipulation functions. Core\nfunctionalities are implemented in 'C++' via 'Rcpp' to ensure\nhigh performance and scalability on large datasets.",
  "URL": "https://csglab.github.io/splikit/,\nhttps://github.com/csglab/splikit",
  "BugReports": "https://github.com/csglab/splikit/issues",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.3",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-13 12:14:01 UTC",
    "User": "root"
  },
  "Author": "Arsham Mikaeili Namini [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9453-6951>)",
  "Maintainer": "Arsham Mikaeili Namini\n<arsham.mikaeilinamini@mail.mcgill.ca>",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-05-13 10:48:18 UTC",
  "RemoteUrl": "https://github.com/cran/splikit",
  "RemoteRef": "HEAD",
  "RemoteSha": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
  "MD5sum": "7a3499a10993273e05b93636bb20e9d4",
  "_user": "cran",
  "_type": "src",
  "_file": "splikit_2.3.1.tar.gz",
  "_fileid": "00a37660e1dfb8c7e95639e3456e59717d74e6b256962ec85d9326c533668329",
  "_filesize": 6374490,
  "_sha256": "00a37660e1dfb8c7e95639e3456e59717d74e6b256962ec85d9326c533668329",
  "_created": "2026-05-13T12:14:01.000Z",
  "_published": "2026-05-22T09:37:46.051Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77354082720,
      "time": 187,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6969801209"
    },
    {
      "job": 77354082253,
      "time": 184,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6969804592"
    },
    {
      "job": 77354082502,
      "time": 187,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6969801514"
    },
    {
      "job": 77354082269,
      "time": 249,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6969823505"
    },
    {
      "job": 77354081560,
      "time": 266,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6969736684"
    },
    {
      "job": 77354081663,
      "time": 143,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7157434455"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/25798160294",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/splikit",
  "_commit": {
    "id": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
    "author": "Arsham Mikaeili Namini <arsham.mikaeilinamini@mail.mcgill.ca>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.3.1\n",
    "time": 1778669298
  },
  "_maintainer": {
    "name": "Arsham Mikaeili Namini",
    "email": "arsham.mikaeilinamini@mail.mcgill.ca",
    "login": "arshammik",
    "orcid": "0000-0002-9453-6951",
    "uuid": 92790984
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-20",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "2.3.1",
      "date": "2026-05-13"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "arshammik",
      "count": 1,
      "uuid": 92790984
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/splikit"
  },
  "_devurl": "https://github.com/csglab/splikit",
  "_pkgdown": "https://csglab.github.io/splikit/",
  "_searchresults": 6,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_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/splikit.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "2.3.1",
      "date": "2026-05-13"
    }
  ],
  "_exports": [
    "find_variable_events",
    "find_variable_genes",
    "get_pseudo_correlation",
    "get_rowVar",
    "get_silhouette_mean",
    "load_toy_M1_M2_object",
    "load_toy_SJ_object",
    "make_eventdata_plus",
    "make_gene_count",
    "make_junction_ab",
    "make_m1",
    "make_m2",
    "make_velo_count",
    "plot_exclusive_junctions",
    "plot_exclusive_junctions_event",
    "plot_exclusive_junctions_pdf",
    "splikit",
    "SplikitObject"
  ],
  "_help": [
    {
      "page": "find_variable_events",
      "title": "Calculate the Sum Deviance for Inclusion and Exclusion Matrices",
      "topics": [
        "find_variable_events"
      ]
    },
    {
      "page": "find_variable_genes",
      "title": "Find Variable Genes Using Variance or Deviance-Based Metrics",
      "topics": [
        "find_variable_genes"
      ]
    },
    {
      "page": "get_pseudo_correlation",
      "title": "Compute Pseudo-Correlation Using Beta-Binomial Model",
      "topics": [
        "get_pseudo_correlation"
      ]
    },
    {
      "page": "get_rowVar",
      "title": "Calculate Row-wise Variance for Dense or Sparse Matrices",
      "topics": [
        "get_rowVar"
      ]
    },
    {
      "page": "get_silhouette_mean",
      "title": "Compute Average Silhouette Width with Logging",
      "topics": [
        "get_silhouette_mean"
      ]
    },
    {
      "page": "load_toy_M1_M2_object",
      "title": "Load the toy M1/M2 object",
      "topics": [
        "load_toy_M1_M2_object"
      ]
    },
    {
      "page": "load_toy_SJ_object",
      "title": "Load the toy SJ object",
      "topics": [
        "load_toy_SJ_object"
      ]
    },
    {
      "page": "make_eventdata_plus",
      "title": "make_eventdata_plus",
      "topics": [
        "make_eventdata_plus"
      ]
    },
    {
      "page": "make_gene_count",
      "title": "make_gene_count",
      "topics": [
        "make_gene_count"
      ]
    },
    {
      "page": "make_junction_ab",
      "title": "make_junction_ab",
      "topics": [
        "make_junction_ab"
      ]
    },
    {
      "page": "make_m1",
      "title": "make_m1",
      "topics": [
        "make_m1"
      ]
    },
    {
      "page": "make_m2",
      "title": "make_m2 (Integrated with Automatic Batching)",
      "topics": [
        "make_m2"
      ]
    },
    {
      "page": "make_velo_count",
      "title": "Process Spliced and Unspliced Counts from Velocyto Outputs",
      "topics": [
        "make_velo_count"
      ]
    },
    {
      "page": "plot_exclusive_junctions",
      "title": "Plot transcript-exclusive splice junctions",
      "topics": [
        "plot_exclusive_junctions"
      ]
    },
    {
      "page": "plot_exclusive_junctions_event",
      "title": "Plot transcript-exclusive splice junctions observed in eventdata",
      "topics": [
        "plot_exclusive_junctions_event"
      ]
    },
    {
      "page": "plot_exclusive_junctions_pdf",
      "title": "Multi-page PDF of transcript-exclusive junctions",
      "topics": [
        "plot_exclusive_junctions_pdf"
      ]
    },
    {
      "page": "print.splikit_junction_plot",
      "title": "Print method for splikit junction-plot results",
      "topics": [
        "print.splikit_junction_plot"
      ]
    },
    {
      "page": "splikit",
      "title": "Create a SplikitObject",
      "topics": [
        "splikit"
      ]
    },
    {
      "page": "SplikitObject",
      "title": "SplikitObject",
      "topics": [
        "SplikitObject"
      ]
    }
  ],
  "_pkglogo": "https://github.com/cran/splikit/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/cran/splikit/raw/HEAD/README.md",
  "_rundeps": [
    "data.table",
    "lattice",
    "Matrix",
    "R6",
    "Rcpp",
    "RcppArmadillo"
  ],
  "_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"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "methods.Rmd",
      "filename": "methods.html",
      "title": "Methods Overview",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Methods Overview",
        "Local junction variants (LJVs)",
        "Variable-event selection",
        "Variable-gene selection",
        "Event-covariate association",
        "Implementation"
      ],
      "created": "2026-05-13 10:48:18",
      "modified": "2026-05-13 10:48:18",
      "commits": 1
    },
    {
      "source": "splikit_manual.Rmd",
      "filename": "splikit_manual.html",
      "title": "Splikit Manual for Single-Cell Splicing Analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Splikit Manual for Single-Cell Splicing Analysis",
        "Table of Contents",
        "Introduction",
        "What Does Splikit Do?",
        "How splikit get these data?",
        "Installation",
        "Prerequisites",
        "Installation from Source",
        "Verify Installation",
        "Core Concepts",
        "Splicing Junction Events",
        "Matrix Representations",
        "Coordinate Groups",
        "Variable Event Detection",
        "Getting Started",
        "Quick Start Workflow",
        "R6 Object-Oriented Interface",
        "Creating a SplikitObject",
        "Complete Workflow with Method Chaining",
        "Step-by-Step Workflow",
        "Subsetting SplikitObjects",
        "Working with Existing Matrices",
        "Accessing SplikitObject Fields",
        "R6 vs Function-Based Interface Comparison",
        "Performance Features",
        "Main Workflow Functions",
        "make_junction_ab()",
        "make_m1()",
        "make_m2()",
        "Additional Data Processing Functions",
        "make_gene_count()",
        "make_velo_count()",
        "Feature Selection Functions",
        "find_variable_events()",
        "find_variable_genes()",
        "Utility Functions",
        "get_pseudo_correlation()",
        "get_rowVar()",
        "get_silhouette_mean()",
        "Complete Workflow Example",
        "Scenario: Analyzing Cell Type-Specific Splicing",
        "Advanced Workflow: Multi-sample Comparison",
        "Advanced Usage",
        "Performance Optimization",
        "Parallel Processing",
        "Memory Management",
        "Integration with Other Packages",
        "Seurat Integration",
        "SingleCellExperiment Integration",
        "Custom Analysis Functions",
        "Differential Splicing Analysis",
        "Troubleshooting",
        "Common Issues and Solutions",
        "Issue 1: Memory Errors with Large Datasets",
        "Issue 2: STARsolo Directory Structure Problems",
        "Issue 3: Barcode Mismatch Issues",
        "Issue 4: Low Event Detection",
        "Performance Benchmarking",
        "Function Reference",
        "Core Workflow Functions",
        "Data Loading Functions",
        "Technical Functions",
        "Conclusion"
      ],
      "created": "2026-05-13 10:48:18",
      "modified": "2026-05-13 10:48:18",
      "commits": 1
    },
    {
      "source": "STARsolo_guide.Rmd",
      "filename": "STARsolo_guide.html",
      "title": "STARsolo Processing Guide for Splicing Analysis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Splicing-Pipeline",
        "1. Mapping using STARsolo"
      ],
      "created": "2026-05-13 10:48:18",
      "modified": "2026-05-13 10:48:18",
      "commits": 1
    }
  ],
  "_score": 3.1760912590556813,
  "_indexed": true,
  "_nocasepkg": "splikit",
  "_universes": [
    "cran",
    "arshammik",
    "csglab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.3.1",
      "date": "2026-05-13T12:17:02.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
      "fileid": "1c81d154092b36aab1f9d14b01a44772c10da27153a535e90cf7efb32f842f43",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25798160294"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.3.1",
      "date": "2026-05-13T12:17:04.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
      "fileid": "0bc15dd5b3df78f644d5000acd62d17d6065a97c179bc6acf9498bfd3f0a1bb6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25798160294"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.3.1",
      "date": "2026-05-13T12:17:00.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
      "fileid": "85831660cb4267673dea5bad3b519e53e2cabe184c545a0da40b6acf7964a8a9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25798160294"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.3.1",
      "date": "2026-05-13T12:17:55.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
      "fileid": "109105d48254ff6da58ddc39d14df65bf34e32b44e210b0ba8437cd5445651ee",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25798160294"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.3.1",
      "date": "2026-05-22T09:36:52.000Z",
      "arch": "emscripten",
      "commit": "464cc6753bc0787f1b810ffb9a7fdb7a98dcc840",
      "fileid": "84202d64c039f50215717e0599012b3ceab36243ec7f23848f61e277c32cb4f6",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25798160294"
    }
  ]
}