{
  "_id": "6a27bf9f24555f66ed53ca6b",
  "Package": "cinaR",
  "Type": "Package",
  "Title": "A Computational Pipeline for Bulk 'ATAC-Seq' Profiles",
  "Version": "0.2.6",
  "Authors@R": "c(person(given = \"Onur\",\nfamily = \"Karakaslar\",\nrole = c(\"aut\", \"cre\"),\nemail = \"eonurkara@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9182-910X\")),\nperson(given = \"Duygu\",\nfamily = \"Ucar\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-9772-3066\"))\n)",
  "Author": "Onur Karakaslar [aut, cre]\n(<https://orcid.org/0000-0002-9182-910X>), Duygu Ucar [aut]\n(<https://orcid.org/0000-0002-9772-3066>)",
  "Maintainer": "Onur Karakaslar <eonurkara@gmail.com>",
  "Description": "Differential analyses and Enrichment pipeline for bulk\n'ATAC-seq' data analyses. This package combines different\npackages to have an ultimate package for both data analyses and\nvisualization of 'ATAC-seq' data. Methods are described in\n'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://github.com/eonurk/cinaR/, https://eonurk.github.io/cinaR/",
  "BugReports": "https://github.com/eonurk/cinaR/issues/",
  "biocViews": "",
  "RoxygenNote": "7.2.3",
  "VignetteBuilder": "knitr, rmarkdown, markdown",
  "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://eonurk.r-universe.dev",
  "Date/Publication": "2026-02-09 10:26:57 UTC",
  "RemoteUrl": "https://github.com/eonurk/cinar",
  "RemoteRef": "HEAD",
  "RemoteSha": "882ce2920aebec0f2dc8ba022736818a4f7de316",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-09 07:12:00 UTC",
    "User": "root"
  },
  "MD5sum": "538fe545c75699ed09bec930c3124538",
  "_user": "eonurk",
  "_type": "src",
  "_file": "cinaR_0.2.6.tar.gz",
  "_fileid": "20ac0df1aefce5c1c35be9ff27545c28a7692ee1a470a5cc24c4f79d92cc59ae",
  "_filesize": 2854925,
  "_sha256": "20ac0df1aefce5c1c35be9ff27545c28a7692ee1a470a5cc24c4f79d92cc59ae",
  "_created": "2026-06-09T07:12:00.000Z",
  "_published": "2026-06-09T07:24:15.213Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 80267925049,
      "time": 304,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7500938467"
    },
    {
      "job": 80267925029,
      "time": 294,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500934873"
    },
    {
      "job": 80267925053,
      "time": 290,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7501052857"
    },
    {
      "job": 80267925055,
      "time": 182,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7501022233"
    },
    {
      "job": 80266750089,
      "time": 463,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500841679"
    },
    {
      "job": 80267925088,
      "time": 282,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500930924"
    },
    {
      "job": 80267925041,
      "time": 204,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7500906271"
    },
    {
      "job": 80267925051,
      "time": 204,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7500906903"
    },
    {
      "job": 80267925069,
      "time": 247,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7500921018"
    }
  ],
  "_buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/eonurk/cinar",
  "_commit": {
    "id": "882ce2920aebec0f2dc8ba022736818a4f7de316",
    "author": "eonurk <onurkara3594@gmail.com>",
    "committer": "eonurk <onurkara3594@gmail.com>",
    "message": "Add LLM index and MCP starter schemas\n",
    "time": 1770632817
  },
  "_maintainer": {
    "name": "Onur Karakaslar",
    "email": "eonurkara@gmail.com",
    "orcid": "0000-0002-9182-910X"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0.0",
      "role": "Depends"
    },
    {
      "package": "BiocManager",
      "role": "Imports"
    },
    {
      "package": "DESeq2",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "fgsea",
      "role": "Imports"
    },
    {
      "package": "GenomicRanges",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "ggrepel",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "limma",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "preprocessCore",
      "role": "Imports"
    },
    {
      "package": "RColorBrewer",
      "role": "Imports"
    },
    {
      "package": "sva",
      "role": "Imports"
    },
    {
      "package": "writexl",
      "role": "Imports"
    },
    {
      "package": "ChIPseeker",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "Matrix",
      "role": "Suggests"
    },
    {
      "package": "Seurat",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "markdown",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg38.knownGene",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Hsapiens.UCSC.hg19.knownGene",
      "role": "Suggests"
    },
    {
      "package": "TxDb.Mmusculus.UCSC.mm10.knownGene",
      "role": "Suggests"
    }
  ],
  "_owner": "eonurk",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-06",
      "n": 8
    },
    {
      "week": "2026-07",
      "n": 1
    }
  ],
  "_tags": [],
  "_topics": [
    "atac-seq",
    "differential-analysis",
    "enrichment-analysis",
    "gene-sets"
  ],
  "_stars": 16,
  "_contributors": [
    {
      "user": "eonurk",
      "count": 44,
      "uuid": 22842930
    }
  ],
  "_userbio": {
    "uuid": 22842930,
    "type": "user",
    "name": "Onur Karakaslar",
    "description": "PhD in CS @ LUMC & TU Delft | Comp. Bio, AI, ML"
  },
  "_downloads": {
    "count": 229,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/cinaR"
  },
  "_devurl": "https://github.com/eonurk/cinar",
  "_pkgdown": "https://eonurk.github.io/cinaR/",
  "_searchresults": 56,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/cinaR.html",
    "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",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/eonurk/cinar",
  "_realowner": "eonurk",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2020-11-14"
    },
    {
      "version": "0.2.0",
      "date": "2021-01-05"
    },
    {
      "version": "0.2.1",
      "date": "2021-04-02"
    },
    {
      "version": "0.2.3",
      "date": "2022-05-18"
    },
    {
      "version": "0.2.6",
      "date": "2026-02-04"
    }
  ],
  "_exports": [
    "cinaR",
    "color_values",
    "dot_plot",
    "filterConsensus",
    "GSEA",
    "heatmap_differential",
    "heatmap_var_peaks",
    "HPEA",
    "normalizeConsensus",
    "pca_plot",
    "prep_scATAC_cinaR",
    "prep_scATAC_seurat",
    "run_enrichment",
    "scale_rows",
    "show_comparisons",
    "verboseFn"
  ],
  "_datasets": [
    {
      "name": "bed",
      "title": "Example peaks from bone marrow of B6 mice",
      "object": "atac_seq_consensus_bm",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Chr",
        "Start",
        "End",
        "B6-18mo-M-BM-47-GT18-01783",
        "B6-18mo-F-BM-42-GT18-01780",
        "B6-18mo-M-BM-45-GT18-01781",
        "B6-18mo-F-BM-40-GT18-01778",
        "B6-18mo-F-BM-41-GT18-01779",
        "NZO-18mo-F-BM-35-GT18-03804",
        "NZO-18mo-F-BM-36-GT18-03805",
        "NZO-18mo-F-BM-42-GT18-03806",
        "NZO-18mo-M-BM-38-GT18-03807",
        "NZO-18mo-M-BM-39-GT18-03808",
        "NZO-18mo-M-BM-40-GT18-03809",
        "B6-3mo-F-BM-4-GT18-04678",
        "B6-3mo-F-BM-5-GT18-04679",
        "B6-3mo-M-BM-1-GT18-04680",
        "B6-3mo-M-BM-2-GT18-04681",
        "B6-3mo-M-BM-3-GT18-04682",
        "NZO-3mo-F-BM-245-GT18-10918",
        "NZO-3mo-F-BM-243-GT18-10916",
        "NZO-3mo-M-BM-251-GT18-10919",
        "NZO-3mo-M-BM-253-GT18-10921",
        "NZO-3mo-F-BM-244-GT18-10917",
        "NZO-3mo-M-BM-252-GT18-10920"
      ],
      "rows": 1000,
      "table": true,
      "tojson": true
    },
    {
      "name": "grch37",
      "title": "Grch37",
      "object": "grch37",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "ensgene",
        "entrez",
        "symbol"
      ],
      "rows": 66978,
      "table": true,
      "tojson": true
    },
    {
      "name": "grch38",
      "title": "Grch38",
      "object": "grch38",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "ensgene",
        "entrez",
        "symbol"
      ],
      "rows": 67495,
      "table": true,
      "tojson": true
    },
    {
      "name": "grcm38",
      "title": "Grcm38",
      "object": "grcm38",
      "class": [
        "data.frame"
      ],
      "fields": [
        "symbol",
        "ensgene",
        "entrez",
        "HGNC.symbol"
      ],
      "rows": 25350,
      "table": true,
      "tojson": true
    },
    {
      "name": "vp2008",
      "title": "Immune modules",
      "object": "VP2008",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "annotatePeaks",
      "title": "annotatePeaks",
      "topics": [
        "annotatePeaks"
      ]
    },
    {
      "page": "bed",
      "title": "Example peaks from bone marrow of B6 mice",
      "topics": [
        "bed"
      ]
    },
    {
      "page": "cinaR",
      "title": "cinaR",
      "topics": [
        "cinaR"
      ]
    },
    {
      "page": "color_values",
      "title": "color values",
      "topics": [
        "color_values"
      ]
    },
    {
      "page": "differentialAnalyses",
      "title": "Differential Analyses",
      "topics": [
        "differentialAnalyses"
      ]
    },
    {
      "page": "dot_plot",
      "title": "dot_plot",
      "topics": [
        "dot_plot"
      ]
    },
    {
      "page": "filterConsensus",
      "title": "filterConsensus",
      "topics": [
        "filterConsensus"
      ]
    },
    {
      "page": "grch37",
      "title": "Grch37",
      "topics": [
        "grch37"
      ]
    },
    {
      "page": "grch38",
      "title": "Grch38",
      "topics": [
        "grch38"
      ]
    },
    {
      "page": "grcm38",
      "title": "Grcm38",
      "topics": [
        "grcm38"
      ]
    },
    {
      "page": "GSEA",
      "title": "GSEA",
      "topics": [
        "GSEA"
      ]
    },
    {
      "page": "heatmap_differential",
      "title": "heatmap_differential",
      "topics": [
        "heatmap_differential"
      ]
    },
    {
      "page": "heatmap_var_peaks",
      "title": "heatmap_var_peaks",
      "topics": [
        "heatmap_var_peaks"
      ]
    },
    {
      "page": "HPEA",
      "title": "HPEA",
      "topics": [
        "HPEA"
      ]
    },
    {
      "page": "normalizeConsensus",
      "title": "normalizeConsensus",
      "topics": [
        "normalizeConsensus"
      ]
    },
    {
      "page": "pca_plot",
      "title": "pca_plot",
      "topics": [
        "pca_plot"
      ]
    },
    {
      "page": "prep_scATAC_cinaR",
      "title": "prep_scATAC_cinaR",
      "topics": [
        "prep_scATAC_cinaR"
      ]
    },
    {
      "page": "prep_scATAC_seurat",
      "title": "prep_scATAC_seurat",
      "topics": [
        "prep_scATAC_seurat"
      ]
    },
    {
      "page": "run_enrichment",
      "title": "run_enrichment",
      "topics": [
        "run_enrichment"
      ]
    },
    {
      "page": "scale_rows",
      "title": "scale_rows",
      "topics": [
        "scale_rows"
      ]
    },
    {
      "page": "show_comparisons",
      "title": "show_comparisons",
      "topics": [
        "show_comparisons"
      ]
    },
    {
      "page": "verboseFn",
      "title": "verboseFn",
      "topics": [
        "verboseFn"
      ]
    },
    {
      "page": "vp2008",
      "title": "Immune modules",
      "topics": [
        "vp2008"
      ]
    }
  ],
  "_readme": "https://github.com/eonurk/cinar/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocManager",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "codetools",
    "cowplot",
    "cpp11",
    "crayon",
    "curl",
    "data.table",
    "DBI",
    "DelayedArray",
    "DESeq2",
    "dplyr",
    "edgeR",
    "farver",
    "fastmap",
    "fastmatch",
    "fgsea",
    "formatR",
    "futile.logger",
    "futile.options",
    "genefilter",
    "generics",
    "GenomicRanges",
    "ggplot2",
    "ggrepel",
    "glue",
    "gtable",
    "httr",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lambda.r",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mgcv",
    "mime",
    "nlme",
    "openssl",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "png",
    "preprocessCore",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "snow",
    "SparseArray",
    "statmod",
    "SummarizedExperiment",
    "survival",
    "sva",
    "sys",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "writexl",
    "XML",
    "xtable",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "cinaR.Rmd",
      "filename": "cinaR.html",
      "title": "Introduction to cinaR",
      "author": "E Onur Karakaslar",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Quick Start",
        "PCA Plots",
        "Heatmaps",
        "Differential peaks",
        "Most variable peaks",
        "Enrichment Plots",
        "Creating different contrasts",
        "Comparison scheme",
        "Running for bulk RNA-seq data",
        "Single-cell ATAC-seq (10x scATAC) preprocessing",
        "Running enrichment with different dataset",
        "cinaRgenesets",
        "MSigDB",
        "Custom gene sets",
        "Selecting different reference genomes",
        "Batch Effect Correction",
        "Adding extra covariates",
        "Saving DA peaks to excel",
        "Using different GLM algorithms",
        "Some useful arguments",
        "References",
        "Session Info"
      ],
      "created": "2020-10-18 00:43:38",
      "modified": "2026-02-02 12:25:27",
      "commits": 20
    }
  ],
  "_score": 5.952308009662125,
  "_indexed": true,
  "_nocasepkg": "cinar",
  "_universes": [
    "eonurk"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.2.6",
      "date": "2026-06-09T07:16:55.000Z",
      "distro": "noble",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "ccad19426824ae67884f658be4b9ea4847485f27356b14575cbcada066fe5c29",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.2.6",
      "date": "2026-06-09T07:16:46.000Z",
      "distro": "noble",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "05271d41b98648ae4071a1f1eaecca21b07aa335001e74dbd5b419502f211a3f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.2.6",
      "date": "2026-06-09T07:22:38.000Z",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "05b2b68ff833e9a40df8657b203ee1ecc391cb817c48478a4e499586d81aad84",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.2.6",
      "date": "2026-06-09T07:21:26.000Z",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "2caeaa999901adc98479f46acdf39837273a19712047e2c7483cb129f0647945",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.2.6",
      "date": "2026-06-09T07:17:04.000Z",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "a6b84652f5690eeca17147fc98785f6317f790bd30cce8fca48bc0335af18bae",
      "status": "success",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.2.6",
      "date": "2026-06-09T07:15:10.000Z",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "cd44f602d40277046b99a0d3a7808d7af39bc72e070d6cb799186fc41d27eb0e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.2.6",
      "date": "2026-06-09T07:15:11.000Z",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "81419f8e2c2072884b77b284cbf693d6aabbbcf307122c0aaada3d091a43e171",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.2.6",
      "date": "2026-06-09T07:15:53.000Z",
      "commit": "882ce2920aebec0f2dc8ba022736818a4f7de316",
      "fileid": "e933711d56e2741f528ae1328b4c3bbf4a0a66351c39e5349e3e8205b9e316ed",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/eonurk/actions/runs/27189703647"
    }
  ]
}