{
  "_id": "6a17ed8facfb0bcc41da4c0b",
  "Package": "colocr",
  "Type": "Package",
  "Title": "Conduct Co-Localization Analysis of Fluorescence Microscopy\nImages",
  "Version": "0.1.1",
  "License": "GPL-3",
  "Authors@R": "person(\"Mahmoud\", \"Ahmed\",\nemail = \"mahmoud.s.fahmy@students.kasralainy.edu.eg\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4377-6541\"))",
  "URL": "https://docs.ropensci.org/colocr,\nhttps://github.com/ropensci/colocr",
  "BugReports": "https://github.com/ropensci/colocr/issues",
  "Description": "Automate the co-localization analysis of fluorescence\nmicroscopy images. Selecting regions of interest, extract pixel\nintensities from the image channels and calculate different\nco-localization statistics. The methods implemented in this\npackage are based on Dunn et al. (2011)\n<doi:10.1152/ajpcell.00462.2010>.",
  "Encoding": "UTF-8",
  "RoxygenNote": "6.1.1",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libfftw3-dev libglpk-dev make libmagick++-dev\ngsfonts libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libxml2-dev libssl-dev libx11-dev zlib1g-dev",
  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2020-01-04 04:10:25 UTC",
  "RemoteUrl": "https://github.com/ropensci/colocr",
  "RemoteRef": "master",
  "RemoteSha": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-28 07:05:35 UTC",
    "User": "root"
  },
  "Author": "Mahmoud Ahmed [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4377-6541>)",
  "Maintainer": "Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>",
  "MD5sum": "aa3af3c35181bcee03c40263ea211020",
  "_user": "ropensci",
  "_type": "src",
  "_file": "colocr_0.1.1.tar.gz",
  "_fileid": "ed19b1aa3aacb2c6412ea074ab6f615fe677a19773f4a0af6b1dc1cf52881770",
  "_filesize": 6890792,
  "_sha256": "ed19b1aa3aacb2c6412ea074ab6f615fe677a19773f4a0af6b1dc1cf52881770",
  "_created": "2026-05-28T07:05:35.000Z",
  "_published": "2026-05-28T07:23:59.066Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 78240789837,
      "time": 187,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259744645"
    },
    {
      "job": 78240789853,
      "time": 191,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259745831"
    },
    {
      "job": 78240789909,
      "time": 119,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259983090"
    },
    {
      "job": 78240789804,
      "time": 133,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259958043"
    },
    {
      "job": 78240097789,
      "time": 180,
      "config": "pkgdown",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259660300"
    },
    {
      "job": 78240097798,
      "time": 313,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259693933"
    },
    {
      "job": 78240789877,
      "time": 137,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7259731503"
    },
    {
      "job": 78240789812,
      "time": 149,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7259734389"
    },
    {
      "job": 78240789840,
      "time": 239,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7259758513"
    },
    {
      "job": 78240789831,
      "time": 143,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7259733123"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/ropensci/colocr",
  "_commit": {
    "id": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
    "author": "MahShaaban <mahmoud.s.fahmy@students.kasralainy.edu.eg>",
    "committer": "MahShaaban <mahmoud.s.fahmy@students.kasralainy.edu.eg>",
    "message": "Minor changes for v0.1.1\n\t- Skip app testing on CRAN\n\t- Add related article citation information\n\t- Updated readme and news\n",
    "time": 1578111025
  },
  "_maintainer": {
    "name": "Mahmoud Ahmed",
    "email": "mahmoud.s.fahmy@students.kasralainy.edu.eg",
    "login": "mahshaaban",
    "description": "Postdoc",
    "uuid": 16605756,
    "orcid": "0000-0002-4377-6541"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "imager",
      "role": "Imports"
    },
    {
      "package": "magick",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "shinytest",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "devtools",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "shinyBS",
      "role": "Suggests"
    }
  ],
  "_owner": "ropensci",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "colocalization",
    "image-analysis"
  ],
  "_stars": 26,
  "_contributors": [
    {
      "user": "mahshaaban",
      "count": 21,
      "uuid": 16605756
    }
  ],
  "_userbio": {
    "uuid": 1200269,
    "type": "organization",
    "name": "rOpenSci",
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 20,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/colocr"
  },
  "_mentions": 2,
  "_devurl": "https://github.com/ropensci/colocr",
  "_pkgdown": "https://docs.ropensci.org/colocr",
  "_searchresults": 25,
  "_metadata": {
    "review": {
      "id": 243,
      "status": "reviewed",
      "version": "0.1.0",
      "organization": "rOpenSci Software Review",
      "url": "https://github.com/ropensci/software-review/issues/243"
    },
    "ropensci_category": "data-extraction"
  },
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/colocr.html",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_realowner": "ropensci",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.1.0",
      "date": "2019-05-31"
    },
    {
      "version": "0.1.1",
      "date": "2020-05-08"
    }
  ],
  "_exports": [
    ".intensity_get",
    ".labels_add",
    ".manders",
    ".pearson",
    "%>%",
    "colocr_app",
    "image_load",
    "roi_check",
    "roi_select",
    "roi_show",
    "roi_test"
  ],
  "_help": [
    {
      "page": "dot-intensity_get",
      "title": "Get pixel intensities",
      "topics": [
        ".intensity_get"
      ]
    },
    {
      "page": "dot-labels_add",
      "title": "Label regions of interest",
      "topics": [
        ".labels_add"
      ]
    },
    {
      "page": "dot-manders",
      "title": "Calculate Marnders Overlap Coefficient",
      "topics": [
        ".manders"
      ]
    },
    {
      "page": "dot-pearson",
      "title": "Calculate Pearson's Correlation Coefficient",
      "topics": [
        ".pearson"
      ]
    },
    {
      "page": "colocr",
      "title": "'colocr': Conduct Co-localization Analysis of Microscopy Images.",
      "topics": [
        "colocr-package",
        "colocr"
      ]
    },
    {
      "page": "colocr_app",
      "title": "Run the shiny App",
      "topics": [
        "colocr_app"
      ]
    },
    {
      "page": "image_load",
      "title": "Load images from files",
      "topics": [
        "image_load"
      ]
    },
    {
      "page": "roi_check",
      "title": "Show pixel intensities",
      "topics": [
        "roi_check"
      ]
    },
    {
      "page": "roi_select",
      "title": "Select regions of interest",
      "topics": [
        "roi_select"
      ]
    },
    {
      "page": "roi_show",
      "title": "Show the selected regions of interest",
      "topics": [
        "roi_show"
      ]
    },
    {
      "page": "roi_test",
      "title": "Test Co-localization",
      "topics": [
        "roi_test"
      ]
    }
  ],
  "_readme": "https://github.com/ropensci/colocr/raw/master/README.md",
  "_rundeps": [
    "base64enc",
    "bmp",
    "bslib",
    "cachem",
    "cli",
    "commonmark",
    "cpp11",
    "curl",
    "digest",
    "downloader",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "glue",
    "htmltools",
    "httpuv",
    "igraph",
    "imager",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "magick",
    "magrittr",
    "Matrix",
    "memoise",
    "mime",
    "otel",
    "pkgconfig",
    "png",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readbitmap",
    "rlang",
    "sass",
    "scales",
    "shiny",
    "sourcetools",
    "stringi",
    "stringr",
    "tiff",
    "vctrs",
    "viridisLite",
    "withr",
    "xtable"
  ],
  "_vignettes": [
    {
      "source": "using_colocr.Rmd",
      "filename": "using_colocr.html",
      "title": "Using colocr",
      "author": "Mahmoud Ahmed",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Getting started",
        "Detailed Example",
        "Choosing ROIs",
        "Calculating Correlation Statistics",
        "Selecting a multiple regions in an image",
        "Analyzing a collection of images at once",
        "Reproducing the shiny app output",
        "Description of the co-localization statistics",
        "PCC",
        "MOC",
        "Colocalization Benchmark Source",
        "Acknowledgement"
      ],
      "created": "2018-07-18 02:57:51",
      "modified": "2019-05-28 01:08:01",
      "commits": 18
    }
  ],
  "_score": 4.812913356642856,
  "_indexed": true,
  "_nocasepkg": "colocr",
  "_universes": [
    "ropensci",
    "mahshaaban"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-28T07:08:11.000Z",
      "distro": "noble",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "362cfe7f7ed74c20b9cd377bf714e28af696c91abd60b6c5f73a71cdabca4709",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.1.1",
      "date": "2026-05-28T07:08:17.000Z",
      "distro": "noble",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "695f4f395baf4d81d08301675975a7b84abf521e0d3a2d11ac800ab3e17d89ab",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-28T07:22:44.000Z",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "6ee42749e81b007d5d145bf9f5cfd96cef1938fdf0179bee4510bf15494c2d78",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.1.1",
      "date": "2026-05-28T07:21:17.000Z",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "2dd7f4f7779e6b2d691042b501e3e379bfcb301d7add484232b5589b69614546",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.1.1",
      "date": "2026-05-28T07:08:15.000Z",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "f30bf1185dd033afbd5b62385c5ab6b3b86c793f28e3f320f79867107dce9b2d",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-28T07:07:03.000Z",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "4d3a1caca9bb069cdb1ff8c75f3e1228e7d4898c810e6a83d2127940f86a63a7",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-28T07:08:30.000Z",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "e1f55d9eec467f611b7fc43fb1f89bc0c8d8813c33ee68f2eb1474d20e6cee28",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.1.1",
      "date": "2026-05-28T07:06:59.000Z",
      "commit": "9b7bd6ef54c7d35b62334e0e140219b5a3853361",
      "fileid": "ee47ac1d6b233b8510d32972648155a6015f8c631a53b18d7a932e2f50ea79c3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/26559868439"
    }
  ]
}