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  "Title": "Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library",
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  "Date": "2026-03-17",
  "Authors@R": "c(person(given = \"Jitao David\",\nfamily = \"Zhang\",\nrole = c(\"aut\", \"cre\", \"ctb\"),\nemail = \"jitao_david.zhang@roche.com\",\ncomment = c(ORCID=\"0000-0002-3085-0909\")),\nperson(given = \"Clemens\",\nfamily = \"Broger\",\nrole = c(\"aut\", \"ctb\")),\nperson(\"F.Hoffmann-La Roche AG\", role=\"cph\"),\nperson(given=\"Junio C\", family=\"Hamano\", role=\"cph\"),\nperson(given=\"Jean\", family=\"Thierry-Mieg\", role=\"cph\"),\nperson(given=\"Konrad\", family=\"Rudolph\", role=\"cph\"),\nperson(given=\"Richard\", family=\"Durbin\", role=\"cph\"))",
  "Description": "Provides interface to the 'Bioinfo-C' (internal name:\n'BIOS') library and utilities. 'ribiosUtils' is a Swiss-knife\nfor computational biology in drug discovery, providing\nfunctions and utilities with minimal external dependency and\nmaximal efficiency.",
  "License": "GPL-3",
  "URL": "https://github.com/bedapub/ribiosUtils,\nhttps://bedapub.github.io/ribiosUtils/",
  "BugReports": "https://github.com/bedapub/ribiosUtils/issues",
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  "Author": "Jitao David Zhang [aut, cre, ctb] (ORCID:\n<https://orcid.org/0000-0002-3085-0909>),\nClemens Broger [aut, ctb],\nF.Hoffmann-La Roche AG [cph],\nJunio C Hamano [cph],\nJean Thierry-Mieg [cph],\nKonrad Rudolph [cph],\nRichard Durbin [cph]",
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  "_published": "2026-06-02T18:16:06.662Z",
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  },
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  "_assets": [
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    "extra/citation.json",
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    "extra/NEWS.txt",
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    "extra/readme.md",
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    "manual.pdf"
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  ],
  "_exports": [
    "allIdentical",
    "apply1",
    "apply2",
    "applyTopOrIncAndNotExclFilter",
    "asNumMatrix",
    "assertColumnName",
    "assertContrast",
    "assertDesign",
    "assertDesignContrast",
    "assertDir",
    "assertFile",
    "basefilename",
    "bedaInfo",
    "biomicsPstorePath2URL",
    "bound",
    "boundNorm",
    "cbindByRownames",
    "checkDir",
    "checkFile",
    "chosenFew",
    "clearLog",
    "closeLoggerConnections",
    "columnOverlapCoefficient",
    "compTwoVecs",
    "corByRownames",
    "countTokens",
    "createDir",
    "createRmdTemplate",
    "cumJaccardDistance",
    "cumJaccardIndex",
    "cumOverlapCoefficient",
    "cumOverlapDistance",
    "cumsumprop",
    "cutInterval",
    "cutreeIntoOrderedGroups",
    "dfFactor",
    "dfFactor2Str",
    "doLog",
    "equateWellLabelWidth",
    "extname",
    "firstUp",
    "fixWidthStr",
    "flushLog",
    "haltifnot",
    "headhead",
    "headtail",
    "identicalMatrix",
    "identicalMatrixValue",
    "imatch",
    "imatchv",
    "invertList",
    "ipmatch",
    "ipmatchv",
    "isDebugging",
    "isDir",
    "isError",
    "isEven",
    "isIntDebugging",
    "isInvarCol",
    "isMaxStatRow",
    "isOdd",
    "isRocheCompoundID",
    "isTopOrIncAndNotExcl",
    "isVarCol",
    "jaccardDistance",
    "jaccardIndex",
    "keepMaxStatRow",
    "keepMaxStatRowInd",
    "lastChar",
    "libordie",
    "list2df",
    "listOverlapCoefficient",
    "longdf2matrix",
    "matchColumn",
    "matchColumnIndex",
    "matchColumnName",
    "matchv",
    "matrix2longdf",
    "mergeInfreqLevelsByCumsumprop",
    "midentical",
    "mintersect",
    "mmatch",
    "mset",
    "msetdiff",
    "munion",
    "na.false",
    "naivePairwiseDist",
    "nField",
    "ofactor",
    "overlapCoefficient",
    "overlapDistance",
    "overwriteDir",
    "pAbsLog10Score",
    "pairwiseJaccardDistance",
    "pairwiseJaccardIndex",
    "pairwiseOverlapCoefficient",
    "pairwiseOverlapDistance",
    "percentage",
    "pQnormScore",
    "pScore",
    "putColsFirst",
    "pwdecode",
    "pwencode",
    "qqmsg",
    "qsystem",
    "rbindByColnames",
    "refactorNum",
    "registerLog",
    "relevels",
    "relevelsByNamedVec",
    "relevelsByNotNamedVec",
    "reload",
    "removeColumns",
    "removeColumnsByFunc",
    "removeColumnsWithNA",
    "removeInvarCol",
    "removeRowsByFunc",
    "removeRowsWithNA",
    "replaceColumnName",
    "replaceZeroPvalue",
    "ribiosTempdir",
    "ribiosTempfile",
    "rmat",
    "rocheCore",
    "rowscale",
    "rrank",
    "rrankInd",
    "rsetdiff",
    "scriptInit",
    "setDebug",
    "shortenRocheCompoundID",
    "shortenStr",
    "silencio",
    "sortAndFilterByCumsumprop",
    "sortByCol",
    "sortByDimnames",
    "strtoken",
    "stubborngc",
    "subsetByColumnName",
    "summarizeCols",
    "summarizeColumns",
    "summarizeRows",
    "tailtail",
    "trim",
    "ulen",
    "uniqueLength",
    "uniqueNonNA",
    "unsetDebug",
    "verbose",
    "wellIndex2position",
    "whoami",
    "writeLog"
  ],
  "_help": [
    {
      "page": "allIdentical",
      "title": "Testing whether several objects are all identical with each other",
      "topics": [
        "allIdentical"
      ]
    },
    {
      "page": "applyTopOrIncAndNotExclFilter",
      "title": "Apply isTopOrIncAndNotExcl filter to a matrix",
      "topics": [
        "applyTopOrIncAndNotExclFilter"
      ]
    },
    {
      "page": "asNumMatrix",
      "title": "Convert string-valued data frame or matrix into a numeric matrix",
      "topics": [
        "asNumMatrix",
        "atofMatrix",
        "stringDataFrame2numericMatrix"
      ]
    },
    {
      "page": "assertColumnName",
      "title": "Assert whether the required column names exist",
      "topics": [
        "assertColumnName"
      ]
    },
    {
      "page": "assertContrast",
      "title": "Check dimensionality of contrast matrix",
      "topics": [
        "assertContrast"
      ]
    },
    {
      "page": "assertDesign",
      "title": "Check dimensionality of design matrix",
      "topics": [
        "assertDesign"
      ]
    },
    {
      "page": "assertDesignContrast",
      "title": "Check dimensionality of both design and contrast matrix",
      "topics": [
        "assertDesignContrast"
      ]
    },
    {
      "page": "bedaInfo",
      "title": "Print BEDA project information",
      "topics": [
        "bedaInfo"
      ]
    },
    {
      "page": "biomicsPstorePath2URL",
      "title": "Translate BiOmics-Pathology pstore path to URL",
      "topics": [
        "biomicsPstorePath2URL"
      ]
    },
    {
      "page": "bound",
      "title": "Set boundaries for numeric values, or perform a 0-1 normalization.",
      "topics": [
        "bound",
        "boundNorm"
      ]
    },
    {
      "page": "cbindByRownames",
      "title": "Column bind by rownames",
      "topics": [
        "cbindByRownames",
        "rbindByColnames"
      ]
    },
    {
      "page": "checkFile",
      "title": "Check whether file(s) exist",
      "topics": [
        "assertFile",
        "checkFile"
      ]
    },
    {
      "page": "chosenFew",
      "title": "Print the chosen few items of a long vector",
      "topics": [
        "chosenFew"
      ]
    },
    {
      "page": "closeLoggerConnections",
      "title": "Close connections to all loggers This function closes all open connections set up by loggers It is automatically run at the end of the R session (setup by 'registerLog')",
      "topics": [
        "closeLoggerConnections"
      ]
    },
    {
      "page": "columnOverlapCoefficient",
      "title": "Pairwise jaccard/overlap coefficient can be calculated efficiently using matrix Pairwise overlap coefficient of binary matrix by column",
      "topics": [
        "columnOverlapCoefficient"
      ]
    },
    {
      "page": "compTwoVecs",
      "title": "Compare two vectors by set operations",
      "topics": [
        "compTwoVecs"
      ]
    },
    {
      "page": "corByRownames",
      "title": "Calculate correlation coefficients using common rows of the two matrices",
      "topics": [
        "corByRownames"
      ]
    },
    {
      "page": "countTokens",
      "title": "Count tokens by splitting strings",
      "topics": [
        "countTokens",
        "nField"
      ]
    },
    {
      "page": "createDir",
      "title": "Create a directory if it does not exist, and then make sure the creation was successful.",
      "topics": [
        "createDir"
      ]
    },
    {
      "page": "createRmdTemplate",
      "title": "Copy the skeleton RMarkdown file to a specified location",
      "topics": [
        "createRmdTemplate"
      ]
    },
    {
      "page": "cumJaccardIndex",
      "title": "Cumulative Jaccard Index",
      "topics": [
        "cumJaccardDistance",
        "cumJaccardIndex"
      ]
    },
    {
      "page": "cumOverlapCoefficient",
      "title": "Cumulative overlap coefficient",
      "topics": [
        "cumOverlapCoefficient",
        "cumOverlapDistance"
      ]
    },
    {
      "page": "cumsumprop",
      "title": "Proportion of cumulative sum over sum",
      "topics": [
        "cumsumprop"
      ]
    },
    {
      "page": "cutInterval",
      "title": "Cut a vector of numbers into interval factors.",
      "topics": [
        "cutInterval"
      ]
    },
    {
      "page": "cutreeIntoOrderedGroups",
      "title": "Cut a tree into groups of ordered sizes",
      "topics": [
        "cutreeIntoOrderedGroups"
      ]
    },
    {
      "page": "dfFactor",
      "title": "Get a factor vector for a data.frame",
      "topics": [
        "dfFactor"
      ]
    },
    {
      "page": "dfFactor2Str",
      "title": "Convert factor columns in a data.frame into character strings",
      "topics": [
        "dfFactor2Str"
      ]
    },
    {
      "page": "equateWellLabelWidth",
      "title": "Format labels for wells in microwell plates to equal widths",
      "topics": [
        "equateWellLabelWidth"
      ]
    },
    {
      "page": "extname",
      "title": "Get the base and extension(s) of file name(s)",
      "topics": [
        "basefilename",
        "extname"
      ]
    },
    {
      "page": "firstUp",
      "title": "Make the first alphabet of strings uppercase",
      "topics": [
        "firstUp"
      ]
    },
    {
      "page": "fixWidthStr",
      "title": "Shorten strings to strings with a fix width of characters",
      "topics": [
        "fixWidthStr"
      ]
    },
    {
      "page": "haltifnot",
      "title": "Ensure the Truth of R Expressions and Print Defined Error Message if NOT",
      "topics": [
        "haltifnot"
      ]
    },
    {
      "page": "headhead",
      "title": "head/tail function for matrix or data.frame",
      "topics": [
        "headhead",
        "tailtail"
      ]
    },
    {
      "page": "headtail",
      "title": "Print head and tail elements of a vector",
      "topics": [
        "headtail"
      ]
    },
    {
      "page": "identicalMatrix",
      "title": "Test whether two matrices are identical by values and by dim names",
      "topics": [
        "identicalMatrix"
      ]
    },
    {
      "page": "identicalMatrixValue",
      "title": "Test whether two matrices have the same numerica values given certain accuracy",
      "topics": [
        "identicalMatrixValue"
      ]
    },
    {
      "page": "imatch",
      "title": "Case-insensitive match and pmatch",
      "topics": [
        "imatch",
        "imatchv",
        "ipmatch",
        "ipmatchv",
        "matchv"
      ]
    },
    {
      "page": "invertList",
      "title": "Invert the names and elements of a list",
      "topics": [
        "invertList"
      ]
    },
    {
      "page": "isDir",
      "title": "Checks existing directory",
      "topics": [
        "assertDir",
        "checkDir",
        "isDir"
      ]
    },
    {
      "page": "isError",
      "title": "Tell whether an object is an error",
      "topics": [
        "isError"
      ]
    },
    {
      "page": "isOdd",
      "title": "Whether an integer is odd (or even)",
      "topics": [
        "isEven",
        "isOdd"
      ]
    },
    {
      "page": "isRocheCompoundID",
      "title": "Tell whether a character string is a Roche compound ID",
      "topics": [
        "isRocheCompoundID"
      ]
    },
    {
      "page": "isTopOrIncAndNotExcl",
      "title": "Logical vector of being top or included and not excluded",
      "topics": [
        "isTopOrIncAndNotExcl"
      ]
    },
    {
      "page": "jaccardIndex",
      "title": "Calculate the Jaccard Index between two vectors",
      "topics": [
        "jaccardDistance",
        "jaccardIndex"
      ]
    },
    {
      "page": "keepMaxStatRow",
      "title": "KEEP ROWS WITH THE MAXIMUM STATISTIC",
      "topics": [
        "isMaxStatRow",
        "keepMaxStatRow",
        "keepMaxStatRowInd"
      ]
    },
    {
      "page": "lastChar",
      "title": "Return last characters from strings",
      "topics": [
        "lastChar"
      ]
    },
    {
      "page": "libordie",
      "title": "Load a library mutedly and quit (die) in case of failing",
      "topics": [
        "libordie"
      ]
    },
    {
      "page": "list2df",
      "title": "Transform a list of character strings into a data.frame",
      "topics": [
        "list2df"
      ]
    },
    {
      "page": "listOverlapCoefficient",
      "title": "Pairwise overlap coefficient of lists",
      "topics": [
        "listOverlapCoefficient"
      ]
    },
    {
      "page": "longdf2matrix",
      "title": "Convert a long-format data frame into matrix",
      "topics": [
        "longdf2matrix"
      ]
    },
    {
      "page": "matchColumn",
      "title": "Match a column in data.frame to a master vector",
      "topics": [
        "matchColumn",
        "matchColumnIndex"
      ]
    },
    {
      "page": "matchColumnName",
      "title": "Match a given vector to column names of a data.frame or matrix",
      "topics": [
        "matchColumnName"
      ]
    },
    {
      "page": "matrix2longdf",
      "title": "Transform a matrix into a long-format data.frame",
      "topics": [
        "matrix2longdf"
      ]
    },
    {
      "page": "mergeInfreqLevelsByCumsumprop",
      "title": "Merge infrequent levels by setting the threshold of the proportion of cumulative sum over sum a.k.a. cumsumprop",
      "topics": [
        "mergeInfreqLevelsByCumsumprop"
      ]
    },
    {
      "page": "midentical",
      "title": "Multiple identical",
      "topics": [
        "midentical"
      ]
    },
    {
      "page": "mmatch",
      "title": "Multiple matching",
      "topics": [
        "mmatch"
      ]
    },
    {
      "page": "munion",
      "title": "Operations for multiple sets",
      "topics": [
        "mintersect",
        "mset",
        "msetdiff",
        "munion"
      ]
    },
    {
      "page": "na.false",
      "title": "Replace NA with FALSE",
      "topics": [
        "na.false"
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