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  "Title": "Input/Output Utilities of the 'ribios' Suite",
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  "Date": "2026-01-24",
  "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 = \"Balazs\",\nfamily = \"Banfai\",\nrole = \"ctb\"),\nperson(\"F.Hoffmann-La Roche AG\", role=\"cph\"))",
  "Description": "Provides data structures and functions for file\ninput/output in the 'ribios' software suite, supporting common\nbioinformatics and computational biology file formats, designed\nfor fast loading and high performance with minimal\ndependencies.",
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  "Repository": "https://bedapub.r-universe.dev",
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    "find_ampliseq",
    "find_and_read_ampliseq",
    "gctDesc",
    "GctMatrix",
    "gctMatrix2longdf",
    "getDataDir",
    "iofile",
    "is_cls_file",
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    "isGctFile",
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    "loadObject",
    "loadObjectInEnv",
    "loadRDS",
    "longdf2gctMatrix",
    "read_ampliseq",
    "read_ampliseq_bedcovgct",
    "read_annotated_ampliseq_amplicons",
    "read_bed",
    "read_biokit_exprs",
    "read_chip",
    "read_cls",
    "read_david",
    "read_exprs_matrix",
    "read_factor",
    "read_fasta",
    "read_gct_matrix",
    "read_gctstr_matrix",
    "read_gmt_dataframe",
    "read_gmt_list",
    "read_illumina_sampleSheet",
    "read_pheno",
    "read_pheno_factor",
    "read_raw_ampliseq_amplicons",
    "read_trimmed_lines",
    "readMatrix",
    "readTable",
    "setDataDir",
    "strList2DataFrame",
    "write_annotated_ampliseq_amplicons",
    "write_cls",
    "write_factor",
    "write_fasta",
    "write_gct",
    "write_gmt",
    "write.tableList",
    "writeMatrix",
    "writeMatrix.tableList",
    "writeStrList"
  ],
  "_help": [
    {
      "page": "sub-.GctMatrix",
      "title": "Subsetting for GctMatrix",
      "topics": [
        "[.GctMatrix"
      ]
    },
    {
      "page": "as_numeric_matrix",
      "title": "Transform a data.frame to a numeric matrix without characters coereced as factors",
      "topics": [
        "as_numeric_matrix"
      ]
    },
    {
      "page": "as.matrix.GctMatrix",
      "title": "Coerce a GctMatrix object into a matrix",
      "topics": [
        "as.matrix.GctMatrix"
      ]
    },
    {
      "page": "cbindGct",
      "title": "Column bind (cbind) two GctMatrix objects",
      "topics": [
        "cbindGct"
      ]
    },
    {
      "page": "find_ampliseq",
      "title": "Find and read-in AmpliSeq files",
      "topics": [
        "find_ampliseq",
        "find_and_read_ampliseq",
        "read_ampliseq"
      ]
    },
    {
      "page": "gctDesc",
      "title": "Retrieve feature (row) descriptions from a GctMatrix S3-object",
      "topics": [
        "gctDesc"
      ]
    },
    {
      "page": "GctMatrix",
      "title": "Create a GctMatrix object",
      "topics": [
        "GctMatrix"
      ]
    },
    {
      "page": "gctMatrix2longdf",
      "title": "Convert a GctMatrix into a long data frame",
      "topics": [
        "gctMatrix2longdf"
      ]
    },
    {
      "page": "getDataDir",
      "title": "Get the data directory",
      "topics": [
        "getDataDir"
      ]
    },
    {
      "page": "iofile",
      "title": "Get file names for data import/export",
      "topics": [
        "iofile"
      ]
    },
    {
      "page": "is_factor_file",
      "title": "Check if a file encodes a factor",
      "topics": [
        "is_cls_file",
        "is_factor_file"
      ]
    },
    {
      "page": "isGctFile",
      "title": "Test a file is a GCT file or not",
      "topics": [
        "isGctFile"
      ]
    },
    {
      "page": "loadFile",
      "title": "Attempt to load a binary RData file",
      "topics": [
        "loadFile"
      ]
    },
    {
      "page": "loadObject",
      "title": "Load an object by its name from a RData file",
      "topics": [
        "loadObject"
      ]
    },
    {
      "page": "loadObjectInEnv",
      "title": "Load objects from a RData file and return them in an environment",
      "topics": [
        "loadObjectInEnv"
      ]
    },
    {
      "page": "loadRDS",
      "title": "Load an object from a RDS file and returns a logical flag",
      "topics": [
        "loadRDS"
      ]
    },
    {
      "page": "longdf2gctMatrix",
      "title": "Convert a long data.frame into a GctMatrix",
      "topics": [
        "longdf2gctMatrix"
      ]
    },
    {
      "page": "optional_suppress_warning",
      "title": "Supress warning optionally",
      "topics": [
        "optional_suppress_warning"
      ]
    },
    {
      "page": "print.GctMatrix",
      "title": "Print method for GctMatrix object",
      "topics": [
        "print.GctMatrix"
      ]
    },
    {
      "page": "read_ampliseq_bedcovgct",
      "title": "Read bedcov output of AmpliSeq amplicons and convert them to read counts",
      "topics": [
        "read_ampliseq_bedcovgct"
      ]
    },
    {
      "page": "read_annotated_ampliseq_amplicons",
      "title": "Read AmpliSeq amplicon informaiton from an annotated BED file",
      "topics": [
        "read_annotated_ampliseq_amplicons"
      ]
    },
    {
      "page": "read_bed",
      "title": "Read a BED file",
      "topics": [
        "read_bed"
      ]
    },
    {
      "page": "read_biokit_exprs",
      "title": "qRead BioKit expression file into a data.frame",
      "topics": [
        "read_biokit_exprs"
      ]
    },
    {
      "page": "read_chip",
      "title": "Read CHIP file",
      "topics": [
        "read_chip"
      ]
    },
    {
      "page": "read_david",
      "title": "Read tab-delimited result files from DAVID Bioinformatics Resources",
      "topics": [
        "read_david"
      ]
    },
    {
      "page": "read_exprs_matrix",
      "title": "Read an expression matrix from file",
      "topics": [
        "read_exprs_matrix"
      ]
    },
    {
      "page": "read_factor",
      "title": "Read in a factor writtin in the CLS format",
      "topics": [
        "read_cls",
        "read_factor"
      ]
    },
    {
      "page": "read_fasta",
      "title": "Read (write) FASTA sequences into (from) named character vectors",
      "topics": [
        "read_fasta",
        "write_fasta"
      ]
    },
    {
      "page": "read_gct_matrix",
      "title": "Calling C routine to read GCT file into a matrix",
      "topics": [
        "read_gct",
        "read_gctstr_matrix",
        "read_gct_matrix"
      ]
    },
    {
      "page": "read_gmt_dataframe",
      "title": "Read gene-sets in a GMT file into a data.frame",
      "topics": [
        "read_gmt_dataframe"
      ]
    },
    {
      "page": "read_gmt_list",
      "title": "Calling C routine to read GMT file into a list",
      "topics": [
        "read_gmt",
        "read_gmt_list"
      ]
    },
    {
      "page": "read_illumina_sampleSheet",
      "title": "Read the Data block of Illumina sample sheet as data.frame",
      "topics": [
        "read_illumina_sampleSheet"
      ]
    },
    {
      "page": "read_pheno",
      "title": "Read pheno data from CLS or tab-delimited file",
      "topics": [
        "read_pheno",
        "read_pheno_factor"
      ]
    },
    {
      "page": "read_raw_ampliseq_amplicons",
      "title": "Read AmpliSeq amplicon informaiton from an raw BED file",
      "topics": [
        "read_raw_ampliseq_amplicons"
      ]
    },
    {
      "page": "read_trimmed_lines",
      "title": "Read lines, thereby trimming empty spaces around the strings and removing empty lines",
      "topics": [
        "read_trimmed_lines"
      ]
    },
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      "page": "readMatrix",
      "title": "Read in numeric matrix from tab-delimited format written by 'writeMatrix'",
      "topics": [
        "readMatrix"
      ]
    },
    {
      "page": "readTable",
      "title": "Read in data.frame from tab-delimited format written by 'writeMatrix'",
      "topics": [
        "readTable"
      ]
    },
    {
      "page": "setDataDir",
      "title": "Set the data directory",
      "topics": [
        "setDataDir"
      ]
    },
    {
      "page": "strList2DataFrame",
      "title": "Format a string list into a data.frame",
      "topics": [
        "strList2DataFrame"
      ]
    },
    {
      "page": "write_annotated_ampliseq_amplicons",
      "title": "Write AmpliSeq amplicon informaiton into an annotated BED file",
      "topics": [
        "write_annotated_ampliseq_amplicons"
      ]
    },
    {
      "page": "write_factor",
      "title": "Write a factor in the CLS format",
      "topics": [
        "write_cls",
        "write_factor"
      ]
    },
    {
      "page": "write_gct",
      "title": "Write matrix in GCT file format",
      "topics": [
        "write_gct"
      ]
    },
    {
      "page": "write_gmt",
      "title": "Write a list of gene sets into a GMT file",
      "topics": [
        "write_gmt"
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    {
      "page": "write.tableList",
      "title": "Write a list of data.frames (tables) into files",
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    {
      "page": "writeMatrix",
      "title": "Export matrix into a commonly used tab-delimited format inside Roche Bioinformatics",
      "topics": [
        "writeMatrix"
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    {
      "page": "writeMatrix.tableList",
      "title": "Write a list of data.frames (tables) into file with writeMatrix",
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