{
  "_id": "6ac80025de46216d5edd393f",
  "Package": "MRCCC",
  "Type": "Package",
  "Title": "Bayesian Mendelian Randomization for Causal Cell-Cell\nCommunication",
  "Version": "0.99.4",
  "Authors@R": "c(\nperson(\"Bitan\", \"Sarkar\", email = \"bitansarkar010899@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0000-5178-5934\")),\nperson(\"Yang\", \"Ni\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-0636-2363\")))",
  "Description": "Implements MR-CCC, a Bayesian Mendelian randomization\nframework for inferring causal ligand-receptor signalling\nbetween cell types from population-scale single-cell expression\nand genotype data. For each ligand-receptor-pathway triplet,\ncis-eQTL genotypes instrument ligand expression in the sender\ncell type and receptor expression in the receiver cell type,\nand a working model with a ligand-by-receptor interaction is\nfitted to downstream pathway activity by a blocked Gibbs\nsampler. A spike-and-slab prior on the causal block yields a\nposterior inclusion probability that serves as the\ncommunication score, and the retained draws support credible\nintervals, sign probabilities, the receptor level at which the\nligand effect reverses sign, and Bayesian false discovery rate\ncontrol across many triplets.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, StatisticalMethod, Bayesian, GeneExpression,\nSingleCell, Genetics, SystemsBiology, GeneRegulation",
  "URL": "https://github.com/bitansa/MRCCC",
  "BugReports": "https://github.com/bitansa/MRCCC/issues",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "yes",
  "Config/roxygen2/version": "8.1.0",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-10-08 20:03:06 UTC",
  "RemoteUrl": "https://github.com/BiocStaging/MRCCC",
  "RemoteRef": "HEAD",
  "RemoteSha": "8078793179259416e2e7643070057fadb472410b",
  "Packaged": {
    "Date": "2026-10-08 20:34:06 UTC",
    "User": "root"
  },
  "Author": "Bitan Sarkar [aut, cre] (ORCID:\n<https://orcid.org/0009-0000-5178-5934>),\nYang Ni [aut] (ORCID: <https://orcid.org/0000-0003-0636-2363>)",
  "Maintainer": "Bitan Sarkar <bitansarkar010899@gmail.com>",
  "_user": "biocstaging",
  "_type": "src",
  "_file": "MRCCC_0.99.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/1ecb1f388ee9beb418fb162a9f507861886f76da42606a304ba9f5686bd59ce5",
  "_filesize": 394699,
  "_sha256": "1ecb1f388ee9beb418fb162a9f507861886f76da42606a304ba9f5686bd59ce5",
  "_expires": "2027-01-16T20:42:11.000Z",
  "_created": "2026-10-08T20:34:06.000Z",
  "_published": "2026-10-08T20:42:13.099Z",
  "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 4
  },
  "_upstream": "https://github.com/BiocStaging/MRCCC",
  "_commit": {
    "id": "8078793179259416e2e7643070057fadb472410b",
    "author": "Bitan Sarkar <112052702+bitansa@users.noreply.github.com>",
    "committer": "Bitan Sarkar <112052702+bitansa@users.noreply.github.com>",
    "message": "Version 0.99.4: add preprint DOI to CITATION\n",
    "time": 1791489786
  },
  "_maintainer": {
    "name": "Bitan Sarkar",
    "email": "bitansarkar010899@gmail.com",
    "login": "bitansa",
    "description": "",
    "uuid": 112052702,
    "orcid": "0009-0000-5178-5934"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 113528417144,
      "time": 189,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11577950880"
    },
    {
      "job": 113528417082,
      "time": 233,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11576729858"
    },
    {
      "job": 113528417188,
      "time": 224,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11577836196"
    },
    {
      "job": 113528417135,
      "time": 222,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11577447646"
    },
    {
      "job": 113528417147,
      "time": 300,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11578420068"
    },
    {
      "job": 113528417386,
      "time": 193,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11578190210"
    },
    {
      "job": 113528417364,
      "time": 413,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11577931413"
    },
    {
      "job": 113528417544,
      "time": 265,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11578170310"
    },
    {
      "job": 113528417319,
      "time": 401,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11577966389"
    },
    {
      "job": 113526200279,
      "time": 314,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11576774382"
    },
    {
      "job": 113528417101,
      "time": 134,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11576934500"
    },
    {
      "job": 113528417448,
      "time": 316,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11577891242"
    },
    {
      "job": 113528417359,
      "time": 307,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11578000915"
    },
    {
      "job": 113528417338,
      "time": 221,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11576959563"
    },
    {
      "job": 113528417315,
      "time": 379,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11578285539"
    },
    {
      "job": 113528417304,
      "time": 232,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11577866068"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.4.0",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "withr",
      "version": ">= 2.5.0",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    }
  ],
  "_owner": "biocstaging",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-40",
      "n": 2
    },
    {
      "week": "2026-41",
      "n": 3
    }
  ],
  "_tags": [],
  "_topics": [
    "software",
    "statisticalmethod",
    "bayesian",
    "geneexpression",
    "singlecell",
    "genetics",
    "systemsbiology",
    "generegulation",
    "openblas",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "bitansa",
      "count": 5,
      "uuid": 112052702
    }
  ],
  "_userbio": {
    "uuid": 278472782,
    "type": "organization",
    "name": "BiocStaging",
    "followers": 2
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/MRCCC"
  },
  "_devurl": "https://github.com/bitansa/mrccc",
  "_searchresults": 0,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/MRCCC.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE"
  ],
  "_cranurl": false,
  "_exports": [
    "bayes_fdr",
    "bfdr_threshold_set",
    "credible_intervals",
    "mr_ccc",
    "mr_ccc_gibbs",
    "mrccc_hyperparameters",
    "plot_effect_curve",
    "se_row",
    "sign_probabilities",
    "sign_reversal",
    "simulate_mrccc"
  ],
  "_help": [
    {
      "page": "bayes_fdr",
      "title": "Bayesian false discovery rate of nested PIP-ranked sets",
      "topics": [
        "bayes_fdr"
      ]
    },
    {
      "page": "bfdr_threshold_set",
      "title": "Largest PIP-ranked set with Bayesian FDR at most alpha",
      "topics": [
        "bfdr_threshold_set"
      ]
    },
    {
      "page": "credible_intervals",
      "title": "Credible intervals for the MR-CCC effect sizes",
      "topics": [
        "credible_intervals"
      ]
    },
    {
      "page": "mr_ccc",
      "title": "Fit the MR-CCC model to one ligand-receptor-pathway triplet",
      "topics": [
        "mr_ccc"
      ]
    },
    {
      "page": "mr_ccc_gibbs",
      "title": "Gibbs sampler for the MR-CCC model",
      "topics": [
        "mr_ccc_gibbs"
      ]
    },
    {
      "page": "mrccc_hyperparameters",
      "title": "Hyperparameters of the MR-CCC prior",
      "topics": [
        "mrccc_hyperparameters"
      ]
    },
    {
      "page": "plot_effect_curve",
      "title": "Plot the receptor-modulated ligand effect with a credible band",
      "topics": [
        "plot_effect_curve"
      ]
    },
    {
      "page": "plot.mrccc_fit",
      "title": "Plot the receptor-modulated ligand effect of an MR-CCC fit",
      "topics": [
        "plot.mrccc_fit"
      ]
    },
    {
      "page": "print.mrccc_fit",
      "title": "Print an MR-CCC fit",
      "topics": [
        "print.mrccc_fit"
      ]
    },
    {
      "page": "se_row",
      "title": "Extract one gene from a SummarizedExperiment as a donor-level vector",
      "topics": [
        "se_row"
      ]
    },
    {
      "page": "sign_probabilities",
      "title": "Posterior sign probabilities of the interaction effect",
      "topics": [
        "sign_probabilities"
      ]
    },
    {
      "page": "sign_reversal",
      "title": "Receptor level at which the ligand effect reverses sign",
      "topics": [
        "sign_reversal"
      ]
    },
    {
      "page": "simulate_mrccc",
      "title": "Simulate one ligand-receptor-pathway triplet from the MR-CCC working model",
      "topics": [
        "simulate_mrccc"
      ]
    },
    {
      "page": "summary.mrccc_fit",
      "title": "Summarise an MR-CCC fit",
      "topics": [
        "summary.mrccc_fit"
      ]
    }
  ],
  "_readme": "https://github.com/BiocStaging/MRCCC/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "Biobase",
    "BiocGenerics",
    "cli",
    "cpp11",
    "DelayedArray",
    "farver",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "glue",
    "gtable",
    "IRanges",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "SummarizedExperiment",
    "vctrs",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "MRCCC.Rmd",
      "filename": "MRCCC.html",
      "title": "Introduction to MRCCC",
      "author": "Bitan Sarkar, Yang Ni",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "The model",
        "Simulating a triplet",
        "Fitting the model",
        "Input from a SummarizedExperiment",
        "Posterior summaries",
        "Credible intervals",
        "Sign probabilities of the interaction",
        "Sign-reversal threshold",
        "Effect curve",
        "Choosing the chain length",
        "Screening many triplets",
        "Session information"
      ],
      "created": "2026-09-28 05:19:36",
      "modified": "2026-10-06 17:30:56",
      "commits": 3
    }
  ],
  "_score": 3,
  "_indexed": true,
  "_nocasepkg": "mrccc",
  "_universes": [
    "biocstaging",
    "bitansa"
  ],
  "_previous": "0.99.3",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.4",
      "date": "2026-10-08T20:37:01.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/55388a8298d332effd76156a46fcb2096f33f10fbfc3d9e265d10ec515c0ddc0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:52.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/cd719cb0a79d89f59707b362d823e1cfa42717f2bc939c63454eb295d14b5846",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:56.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/d29e6fa97b08d2a5c24405306c803a21721e0faa35336de0c59d952cac208b2a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.99.4",
      "date": "2026-10-08T20:37:28.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/093cc6102975515d8658c03abe25d46afc6155c74ac7f8a3d79ad88ac45c0f11",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:27.000Z",
      "arch": "aarch64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/baf0d779aa7c406d09b4a5840aaae34279656653e5d6adbd3310335c41da5d76",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.4",
      "date": "2026-10-08T20:38:24.000Z",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/bc8893066237c67ca638f8e3e8c92ef5e473aa680bb37d51b1be31edf15878e4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:39.000Z",
      "arch": "aarch64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/4347a141017c59a2f945be55a19381643766fe82dc054026c0bdce51bb407fc4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.99.4",
      "date": "2026-10-08T20:37:11.000Z",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/2e1c2f26a65798da6ac360c737c70af9b18bff60caa11f4edb23387c654bffbb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:55.000Z",
      "arch": "emscripten",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/9a54bb13bba099c860aa4e2798d7546a738b2bae2869ad27a5073584b1101a2b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-08T20:37:55.000Z",
      "arch": "aarch64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/87f019a741d917fe8012ad0a42b9abf4d13c173fdd37dfcf214cfb3ceb29945f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:05.000Z",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/536333cdd847ef23cbcfc1efda10edb880c993a2f8cbba653bbfb0202db2d0be",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-08T20:35:58.000Z",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/45ecbc6f03ba40634fb97cb26e47fb3e5763a1d4e7d5d8d0ae9bd03f8a804717",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-08T20:39:01.000Z",
      "arch": "aarch64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/514f1b6f47d407e8e404dc14104210d2ec16519c2b3a354ee5a34dade6e837f3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.99.4",
      "date": "2026-10-08T20:36:01.000Z",
      "arch": "x86_64",
      "commit": "8078793179259416e2e7643070057fadb472410b",
      "fileid": "https://r2.ropensci.org/3344de5b43cc2e484a0b8940c46fbffa5a58df31e9b7417a785afd6037b0b300",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37839818828"
    }
  ]
}