{ "_id": "6a1ac28e1d7bb097a09d9d5f", "Package": "MetCirc", "Type": "Package", "Title": "Navigating mass spectral similarity in high-resolution MS/MS\nmetabolomics data metabolomics data", "Version": "1.43.0", "Date": "2024-10-16", "Authors@R": "c(person(given = \"Thomas\", family = \"Naake\",\nemail = \"thomasnaake@googlemail.com\",\nrole = c(\"aut\",\"cre\")),\nperson(given = \"Johannes\", family = \"Rainer\",\nemail = \"johannes.rainer@eurac.edu\",\nrole = \"ctb\"),\nperson(given = \"Emmanuel\", family = \"Gaquerel\",\nemail = \"emmanuel.gaquerel@ibmp-cnrs.unistra.fr\", role = \"aut\"))", "Author": "Thomas Naake , Johannes Rainer\n and Emmanuel Gaquerel\n", "Maintainer": "Thomas Naake ", "VignetteBuilder": "knitr", "biocViews": "ShinyApps, Metabolomics, MassSpectrometry, Visualization", "Description": "MetCirc comprises a workflow to interactively explore\nhigh-resolution MS/MS metabolomics data. MetCirc uses the\nSpectra object infrastructure defined in the package Spectra\nthat stores MS/MS spectra. MetCirc offers functionality to\ncalculate similarity between precursors based on the normalised\ndot product, neutral losses or user-defined functions and\nvisualise similarities in a circular layout. Within the\ninteractive framework the user can annotate MS/MS features\nbased on their similarity to (known) related MS/MS features.", "License": "GPL (>= 3)", "RoxygenNote": "7.2.2", "Config/pak/sysreqs": "cmake make libuv1-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:43:42 UTC", "RemoteUrl": "https://github.com/bioc/MetCirc", "RemoteRef": "HEAD", "RemoteSha": "37bad3d733f8f6b759cac675b363c6316f434ea1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:37:19 UTC", "User": "root" }, "MD5sum": "74481dd6e415d434ce99036418e79359", "_user": "bioc", "_type": "src", "_file": "MetCirc_1.43.0.tar.gz", "_fileid": "d21b32a5b3fd8e15e218fee730f3b2dce2f13a2af1a3f8debff7688395653e3e", "_filesize": 2076646, "_sha256": "d21b32a5b3fd8e15e218fee730f3b2dce2f13a2af1a3f8debff7688395653e3e", "_created": "2026-05-30T07:37:19.000Z", "_published": "2026-05-30T10:57:18.276Z", "_jobs": [ { "job": 78634021565, "time": 175, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7306546944" }, { "job": 78634021594, "time": 315, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306560904" }, { "job": 78634021581, "time": 301, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306559696" }, { "job": 78634021573, "time": 153, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307653140" }, { "job": 78634021562, "time": 214, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307659075" }, { "job": 78633844362, "time": 203, "config": "source", "r": "4.6.0", "check": "ERROR", "artifact": "7306529124" }, { "job": 78634021590, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306543050" }, { "job": 78634021605, "time": 220, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306551540" }, { "job": 78634021588, "time": 204, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306549916" }, { "job": 78634021602, "time": 219, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306551598" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109", "_status": "failure", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/MetCirc", "_commit": { "id": "37bad3d733f8f6b759cac675b363c6316f434ea1", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380222 }, "_maintainer": { "name": "Thomas Naake", "email": "thomasnaake@googlemail.com", "login": "tnaake", "description": "", "uuid": 7208089 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "amap", "version": ">= 0.8", "role": "Depends" }, { "package": "circlize", "version": ">= 0.4.16", "role": "Depends" }, { "package": "scales", "version": ">= 1.3.0", "role": "Depends" }, { "package": "shiny", "version": ">= 1.8.1.1", "role": "Depends" }, { "package": "Spectra", "version": ">= 1.15.3", "role": "Depends" }, { "package": "ggplot2", "version": ">= 3.5.1", "role": "Imports" }, { "package": "MsCoreUtils", "version": ">= 1.17.0", "role": "Imports" }, { "package": "S4Vectors", "version": ">= 0.43.1", "role": "Imports" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "graphics", "version": ">= 4.4", "role": "Suggests" }, { "package": "grDevices", "version": ">= 4.4", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.48", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.2.1.1", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_topics": [ "shinyapps", "metabolomics", "massspectrometry", "visualization" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 426, "source": "https://www.bioconductor.org/packages/stats/bioc/MetCirc" }, "_mentions": 3, "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/MetCirc.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "cart2Polar", "circosLegend", "convertMsp2Spectra", "createLink0df", "createLinkDf", "cutLinkDf", "getLinkDfIndices", "highlight", "minFragCart2Polar", "neutralloss", "orderSimilarityMatrix", "plotCircos", "plotSpectra", "shinyCircos", "thresholdLinkDf" ], "_datasets": [ { "name": "compartmentTissue", "title": "Example data for 'MetCirc': 'compartmentTissue'", "object": "idMSMStissueproject", "file": "idMSMStissueproject.RData", "class": [ "data.frame" ], "fields": [ "mz_rt_pcgroup", "SPL", "PED", "LIM", "COR", "FIL", "NEC", "OVA", "ANT", "STY" ], "rows": 259, "table": true, "tojson": true }, { "name": "convertExampleDF", "title": "Example data for 'MetCirc': convertExampleDF", "object": "convertExampleDF", "file": "convertExampleDF.RData", "class": [ "data.frame" ], "fields": [ "Average Rt(min)", "Average Mz", "Metabolite name", "Adduct ion name", "Spectrum reference file name", "TRI03", "TRI02", "TRI01", "LVS03", "LVS02", "LVS01" ], "rows": 100, "table": true, "tojson": true }, { "name": "msp2spectra", "title": "Example data for 'MetCirc': 'msp2spectra'", "object": "convertMsp2Spectra", "file": "convertMsp2Spectra.RData", "class": [ "data.frame" ], "fields": [ "V1", "V2" ], "rows": 1024, "table": true, "tojson": true }, { "name": "sd01_outputXCMS", "title": "Example data for 'MetCirc': 'sd01_outputXCMS'", "object": "sd01_outputXCMS", "file": "sd01_outputXCMS.RData", "class": [ "data.frame" ], "fields": [ null, "mz", "mzmin", "mzmax", "rt", "rtmin", "rtmax", "npeaks", "Accession.72h", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "isotopes", "adduct", "pcgroup" ], "rows": 1044, "table": true, "tojson": true }, { "name": "sd02_deconvoluted", "title": "Example data for 'MetCirc': sd02_deconvoluted", "object": "sd02_deconvoluted", "file": "sd02_deconvoluted.RData", "class": [ "data.frame" ], "fields": [ "mz", "rt", "intensity", "id" ], "rows": 4743, "table": true, "tojson": true }, { "name": "similarityMat", "title": "Example data for 'MetCirc': 'similarityMat'", "object": "similarityMat", "file": "similarityMat.RData", "class": [ "matrix", "array" ], "fields": [ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57", "58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", "69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79", "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", "90", "91", "92", "93", "94", "95", "96", "97", "98", "99", "100", "101", "102", "103", "104", "105", "106", "107", "108", "109", "110", "111", "112", "113", "114", "115", "116", "117", "118", "119", "120", "121", "122", "123", "124", "125", "126", "127", "128", "129", "130", "131", "132", "133", "134", "135", "136", "137", "138", "139", "140", "141", "142", "143", "144", "145", "146", "147", "148", "149", "150", "151", "152", "153", "154", "155", "156", "157", "158", "159", "160", "161", "162", "163", "164", "165", "166", "167", "168", "169", "170", "171", "172", "173", "174", "175", "176", "177", "178", "179", "180", "181", "182", "183", "184", "185", "186", "187", "188", "189", "190", "191", "192", "193", "194", "195", "196", "197", "198", "199", "200", "201", "202", "203", "204", "205", "206", "207", "208", "209", "210", "211", "212", "213", "214", "215", "216", "217", "218", "219", "220", "221", "222", "223", "224", "225", "226", "227", "228", "229", "230", "231", "232", "233", "234", "235", "236", "237", "238", "239", "240", "241", "242", "243", "244", "245", "246", "247", "248", "249", "250", "251", "252", "253", "254", "255", "256", "257", "258", "259" ], "rows": 259, "table": true, "tojson": true }, { "name": "sps_tissue", "title": "Example data for 'MetCirc': 'sps_tissue'", "object": "spectra", "file": "spectra.RData", "class": [ "Spectra" ], "fields": [], "table": false, "tojson": false }, { "name": "tissue", "title": "Example data for 'MetCirc': 'tissue'", "object": "idMSMStissueproject", "file": "idMSMStissueproject.RData", "class": [ "data.frame" ], "fields": [ "mz", "intensity", "rt", "id", "add", "pcgroup", "iso" ], "rows": 37863, "table": true, "tojson": true } ], "_help": [ { "page": "cart2Polar", "title": "Calculate polar coordinates from cartesian coordinates", "topics": [ "cart2Polar" ] }, { "page": "circosLegend", "title": "Plot a legend for circos plot", "topics": [ "circosLegend" ] }, { "page": "compartmentTissue", "title": "Example data for `MetCirc`: `compartmentTissue`", "topics": [ "compartmentTissue" ] }, { "page": "convertExampleDF", "title": "Example data for `MetCirc`: convertExampleDF", "topics": [ "convertExampleDF" ] }, { "page": "convertMsp2Spectra", "title": "Convert MSP data frame into object of class 'Spectra'", "topics": [ "convertMsp2Spectra" ] }, { "page": "createLink0df", "title": "Create a link matrix", "topics": [ "createLink0df" ] }, { "page": "createLinkDf", "title": "Create a data frame which contains features to link (indices)", "topics": [ "createLinkDf" ] }, { "page": "cutLinkDf", "title": "Create a cut data frame with information on links", "topics": [ "cutLinkDf" ] }, { "page": "getLinkDfIndices", "title": "Get indices in 'linkDf' of feature", "topics": [ "getLinkDfIndices" ] }, { "page": "highlight", "title": "Add links and highlight sectors", "topics": [ "highlight" ] }, { "page": "minFragCart2Polar", "title": "Calculate the nearest feature in polar coordinates given cartesian coordinates", "topics": [ "minFragCart2Polar" ] }, { "page": "msp2spectra", "title": "Example data for `MetCirc`: `msp2spectra`", "topics": [ "msp2spectra" ] }, { "page": "neutralloss", "title": "Calculate similarity based on neutral losses", "topics": [ "neutralloss" ] }, { "page": "orderSimilarityMatrix", "title": "Order columns and rows of a similarity matrix according to m/z, retention time and clustering", "topics": [ "orderSimilarityMatrix" ] }, { "page": "plotCircos", "title": "Circular plot to visualize similarity", "topics": [ "plotCircos" ] }, { "page": "plotSpectra", "title": "Plot pair-wise spectra", "topics": [ "plotSpectra" ] }, { "page": "printInformationSelect", "title": "Display information on connected features of selected features", "topics": [ "printInformationSelect" ] }, { "page": "recordPlotFill_degreeFeatures", "title": "Record a plot of filled features and the degree of features", "topics": [ "recordPlotFill_degreeFeatures" ] }, { "page": "recordPlotHighlight", "title": "Return a 'recordedplot' of 'plotCircos' plot with 'highlight = TRUE'", "topics": [ "recordPlotHighlight" ] }, { "page": "replayPlotAdd", "title": "Plot plotCircos or highlight", "topics": [ "replayPlotAdd" ] }, { "page": "replayPlotOrder", "title": "Wrapper for 'replayPlot'", "topics": [ "replayPlotOrder" ] }, { "page": "sd01_outputXCMS", "title": "Example data for `MetCirc`: `sd01_outputXCMS`", "topics": [ "sd01_outputXCMS" ] }, { "page": "sd02_deconvoluted", "title": "Example data for `MetCirc`: sd02_deconvoluted", "topics": [ "sd02_deconvoluted" ] }, { "page": "select", "title": "Select variable based on condition", "topics": [ "select" ] }, { "page": "shinyCircos", "title": "Interactive visualisation of similarity and navigation of MS/MS features", "topics": [ "shinyCircos" ] }, { "page": "similarityMat", "title": "Example data for `MetCirc`: `similarityMat`", "topics": [ "similarityMat" ] }, { "page": "spectraCondition", "title": "Get MS/MS spectra that are present in condition", "topics": [ "spectraCondition" ] }, { "page": "sps_tissue", "title": "Example data for `MetCirc`: `sps_tissue`", "topics": [ "sps_tissue" ] }, { "page": "thresholdLinkDf", "title": "Threshold a data frame containing information on links", "topics": [ "thresholdLinkDf" ] }, { "page": "tissue", "title": "Example data for `MetCirc`: `tissue`", "topics": [ "tissue" ] }, { "page": "typeMatch_link0", "title": "Get typeMatch and link0 data frame", "topics": [ "typeMatch_link0" ] } ], "_readme": "https://github.com/bioc/MetCirc/raw/HEAD/README.md", "_rundeps": [ "amap", "base64enc", "BH", "BiocGenerics", "BiocParallel", "bslib", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "commonmark", "cpp11", "data.table", "digest", "farver", "fastmap", "fontawesome", "formatR", "fs", "futile.logger", "futile.options", "generics", "ggplot2", "GlobalOptions", "glue", "gtable", "htmltools", "httpuv", "IRanges", "isoband", "jquerylib", "jsonlite", "labeling", "lambda.r", "later", "lifecycle", "magrittr", "MASS", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "otel", "promises", "ProtGenerics", "R6", "rappdirs", "RColorBrewer", "Rcpp", "rlang", "S4Vectors", "S7", "sass", "scales", "shape", "shiny", "snow", "sourcetools", "Spectra", "vctrs", "viridisLite", "withr", "xtable" ], "_score": 3.4771212547196626, "_indexed": true, "_nocasepkg": "metcirc", "_universes": [ "bioc", "tnaake" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.43.0", "date": "2026-05-30T07:40:44.000Z", "distro": "noble", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "b1ca71a241ed70ff69c641cc8efd8c3a018a34c990ca551320caae6aedb61a51", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.6.0", "os": "linux", "version": "1.43.0", "date": "2026-05-30T07:40:37.000Z", "distro": "noble", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "bf30e8df2d308fc2d2e1635422e4447be765e07e0a5d8f6e2f42e313a3d60829", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.5.3", "os": "mac", "version": "1.43.0", "date": "2026-05-30T10:51:26.000Z", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "42242f4938a300111aeb38a015a8fbcf55ac5e06a2c23e6872b57eb7ee2a4249", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.6.0", "os": "mac", "version": "1.43.0", "date": "2026-05-30T10:51:58.000Z", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "daf8e4c081e81c773ae9d960394a3d39a7010d301ea0c8e545aa81ef19cc670d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.6.0", "os": "wasm", "version": "1.43.0", "date": "2026-05-30T07:39:57.000Z", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "748d2f17c8dfa19f604f109003accf2218fdf96e6b0486480afe4902bce29af6", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.7.0", "os": "win", "version": "1.43.0", "date": "2026-05-30T07:39:02.000Z", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "026b672477db557ddea9fee8170c63d1e3225ccc7d231e02dcf7a3dbd69c75c3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.5.3", "os": "win", "version": "1.43.0", "date": "2026-05-30T07:38:51.000Z", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "c2bd4a190bca0d2df6d2e2cdb170db5efcaccf9e61e078d5b682b86c998bc807", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" }, { "r": "4.6.0", "os": "win", "version": "1.43.0", "date": "2026-05-30T07:38:59.000Z", "commit": "37bad3d733f8f6b759cac675b363c6316f434ea1", "fileid": "95d7ff163531bed14c60e88b5713573e94b5e2bacd0c7319ae5397824fa2817a", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26678190109" } ] }