{
  "_id": "6a15e2d4acfb0bcc41d6ba39",
  "Package": "BgeeCall",
  "Type": "Package",
  "Title": "Automatic RNA-Seq present/absent gene expression calls\ngeneration",
  "Version": "1.29.1",
  "Date": "2021-05",
  "Authors@R": "c(person(\"Julien\", \"Wollbrett\",\nrole = c(\"aut\", \"cre\"),\nemail = \"julien.wollbrett@unil.ch\"),\nperson(\"Alessandro\", \"Brandulas Cammarata\", role = \"aut\",\nemail = \"alessandro.brandulascammarata@unil.ch\"),\nperson(\"Sara\", \"Fonseca Costa\", role = \"aut\"),\nperson(\"Julien\", \"Roux\", role = \"aut\"),\nperson(\"Marc\", \"Robinson Rechavi\", role = \"ctb\"),\nperson(\"Frederic\", \"Bastian\", role = \"aut\"))",
  "Description": "BgeeCall allows to generate present/absent gene expression\ncalls without using an arbitrary cutoff like TPM<1. Calls are\ngenerated based on reference intergenic sequences. These\nsequences are generated based on expression of all RNA-Seq\nlibraries of each species integrated in Bgee\n(https://bgee.org).",
  "License": "GPL-3 + file LICENSE",
  "URL": "https://github.com/BgeeDB/BgeeCall",
  "BugReports": "https://github.com/BgeeDB/BgeeCall/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-26 11:34:22 UTC",
  "RemoteUrl": "https://github.com/bioc/BgeeCall",
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  "Packaged": {
    "Date": "2026-05-26 18:04:56 UTC",
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  "Author": "Julien Wollbrett [aut, cre],\nAlessandro Brandulas Cammarata [aut],\nSara Fonseca Costa [aut],\nJulien Roux [aut],\nMarc Robinson Rechavi [ctb],\nFrederic Bastian [aut]",
  "Maintainer": "Julien Wollbrett <julien.wollbrett@unil.ch>",
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    "extra/contents.json",
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    "manual.pdf"
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  "_homeurl": "https://github.com/bgeedb/bgeecall",
  "_realowner": "bioc",
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  "_exports": [
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    "download_fasta_intergenic",
    "download_kallisto",
    "generate_calls_workflow",
    "generate_initial_intergenic_regions",
    "generate_presence_absence",
    "generate_reference_intergenic_regions",
    "generate_slurm_calls",
    "generate_slurm_indexes",
    "get_summary_stats",
    "getIntergenicPrefix",
    "getIntergenicRelease",
    "getRunIds",
    "getSimpleArborescence",
    "getWorkingPath",
    "list_bgee_ref_intergenic_species",
    "list_community_ref_intergenic_species",
    "list_intergenic_release",
    "merge_transcriptome_and_intergenic",
    "merging_libraries",
    "Pvalue_averaging",
    "run_kallisto",
    "run_tximport",
    "setAnnotationFromFile",
    "setAnnotationFromObject",
    "setIntergenicRelease",
    "setOutputDir",
    "setRNASeqLibPath",
    "setRunIds",
    "setSimpleArborescence",
    "setTranscriptomeFromFile",
    "setTranscriptomeFromObject",
    "setWorkingPath"
  ],
  "_help": [
    {
      "page": "AbundanceMetadata-class",
      "title": "AbundanceMetadata s4 class",
      "topics": [
        "AbundanceMetadata",
        "AbundanceMetadata-class"
      ]
    },
    {
      "page": "BgeeCall",
      "title": "generate gene expression calls with BgeeCall",
      "topics": [
        "BgeeCall-package",
        "BgeeCall"
      ]
    },
    {
      "page": "BgeeMetadata-class",
      "title": "BgeeMetadata S4 class",
      "topics": [
        "BgeeMetadata",
        "BgeeMetadata-class"
      ]
    },
    {
      "page": "create_kallisto_index",
      "title": "Create kallisto indexes.",
      "topics": [
        "create_kallisto_index"
      ]
    },
    {
      "page": "download_fasta_intergenic",
      "title": "Download fasta intergenic",
      "topics": [
        "download_fasta_intergenic"
      ]
    },
    {
      "page": "download_kallisto",
      "title": "Download binary version of kallisto.",
      "topics": [
        "download_kallisto"
      ]
    },
    {
      "page": "galaxy_calls",
      "title": "generate calls for galaxy",
      "topics": [
        "galaxy_calls"
      ]
    },
    {
      "page": "generate_calls_workflow",
      "title": "generate present/absent calls",
      "topics": [
        "generate_calls_workflow"
      ]
    },
    {
      "page": "generate_initial_intergenic_regions",
      "title": "generates the initial intergenic regions",
      "topics": [
        "generate_initial_intergenic_regions"
      ]
    },
    {
      "page": "generate_presence_absence",
      "title": "Generate presence absence",
      "topics": [
        "generate_presence_absence"
      ]
    },
    {
      "page": "generate_reference_intergenic_regions",
      "title": "Generates reference intergenic regions by removing outlier intergenics",
      "topics": [
        "generate_reference_intergenic_regions"
      ]
    },
    {
      "page": "generate_slurm_calls",
      "title": "Generate present/absent calls on slurm queuing system",
      "topics": [
        "generate_slurm_calls"
      ]
    },
    {
      "page": "generate_slurm_indexes",
      "title": "Generate all indexes for the abundance quantification step",
      "topics": [
        "generate_slurm_indexes"
      ]
    },
    {
      "page": "get_summary_stats",
      "title": "Gather statistical information",
      "topics": [
        "get_summary_stats"
      ]
    },
    {
      "page": "getIntergenicPrefix",
      "title": "`intergenic_prefix` Getter",
      "topics": [
        "getIntergenicPrefix",
        "getIntergenicPrefix,bgeeMetadata",
        "getIntergenicPrefix,BgeeMetadata-method"
      ]
    },
    {
      "page": "getIntergenicRelease",
      "title": "`intergenic_release` Getter",
      "topics": [
        "getIntergenicRelease",
        "getIntergenicRelease,bgeeMetadata",
        "getIntergenicRelease,BgeeMetadata-method"
      ]
    },
    {
      "page": "getRunIds",
      "title": "`run_ids` Getter",
      "topics": [
        "getRunIds",
        "getRunIds,userMetadata",
        "getRunIds,UserMetadata-method"
      ]
    },
    {
      "page": "getSimpleArborescence",
      "title": "`simple_arborescence` Getter",
      "topics": [
        "getSimpleArborescence",
        "getSimpleArborescence,userMetadata",
        "getSimpleArborescence,UserMetadata-method"
      ]
    },
    {
      "page": "getWorkingPath",
      "title": "`working_path` Getter",
      "topics": [
        "getWorkingPath",
        "getWorkingPath,userMetadata",
        "getWorkingPath,UserMetadata-method"
      ]
    },
    {
      "page": "KallistoMetadata-class",
      "title": "KallistoMetadata S4 class",
      "topics": [
        "KallistoMetadata",
        "KallistoMetadata-class"
      ]
    },
    {
      "page": "list_bgee_ref_intergenic_species",
      "title": "List species having Bgee reference intergenic sequences",
      "topics": [
        "list_bgee_ref_intergenic_species"
      ]
    },
    {
      "page": "list_community_ref_intergenic_species",
      "title": "List species having reference intergenic sequences created by the BgeeCall community",
      "topics": [
        "list_community_ref_intergenic_species"
      ]
    },
    {
      "page": "list_intergenic_release",
      "title": "List reference intergenic releases usable with the BgeeCall package",
      "topics": [
        "list_intergenic_release"
      ]
    },
    {
      "page": "merge_transcriptome_and_intergenic",
      "title": "Merge transcriptome file provided by the user with the Bgee intergenic fasta file.",
      "topics": [
        "merge_transcriptome_and_intergenic"
      ]
    },
    {
      "page": "merging_libraries",
      "title": "Calls of expression in combined libraries",
      "topics": [
        "merging_libraries"
      ]
    },
    {
      "page": "Pvalue_averaging",
      "title": "Pvalue averaging",
      "topics": [
        "Pvalue_averaging"
      ]
    },
    {
      "page": "run_kallisto",
      "title": "Run one kallisto abundance analyse",
      "topics": [
        "run_kallisto"
      ]
    },
    {
      "page": "run_tximport",
      "title": "Run tximport",
      "topics": [
        "run_tximport"
      ]
    },
    {
      "page": "setAnnotationFromFile",
      "title": "Set annotation_object of one UserMetadata object",
      "topics": [
        "setAnnotationFromFile",
        "setAnnotationFromFile,userMetadata,character,character",
        "setAnnotationFromFile,UserMetadata,character,character-method",
        "setAnnotationFromFile,UserMetadata,character,missing-method"
      ]
    },
    {
      "page": "setAnnotationFromObject",
      "title": "Set annotation_object of one UserMetadata object",
      "topics": [
        "setAnnotationFromObject",
        "setAnnotationFromObject,userMetadata,GRanges,character",
        "setAnnotationFromObject,UserMetadata,GRanges,character-method"
      ]
    },
    {
      "page": "setIntergenicRelease",
      "title": "`intergenic_release` Setter",
      "topics": [
        "setIntergenicRelease",
        "setIntergenicRelease,bgeeMetadata,character",
        "setIntergenicRelease,BgeeMetadata,character-method"
      ]
    },
    {
      "page": "setOutputDir",
      "title": "`output_dir` Setter",
      "topics": [
        "setOutputDir",
        "setOutputDir,userMetadata,character",
        "setOutputDir,UserMetadata,character-method"
      ]
    },
    {
      "page": "setRNASeqLibPath",
      "title": "`rnaseq_lib_path` Setter",
      "topics": [
        "setRNASeqLibPath",
        "setRNASeqLibPath,userMetadata,character",
        "setRNASeqLibPath,UserMetadata,character-method"
      ]
    },
    {
      "page": "setRunIds",
      "title": "`run_ids` Setter",
      "topics": [
        "setRunIds",
        "setRunIds,userMetadata,character",
        "setRunIds,UserMetadata,character-method"
      ]
    },
    {
      "page": "setSimpleArborescence",
      "title": "`simple_arborescence` Setter",
      "topics": [
        "setSimpleArborescence",
        "setSimpleArborescence,userMetadata,logical",
        "setSimpleArborescence,UserMetadata,logical-method"
      ]
    },
    {
      "page": "setTranscriptomeFromFile",
      "title": "Set transcriptome_object of one UserMetadata object",
      "topics": [
        "setTranscriptomeFromFile",
        "setTranscriptomeFromFile,userMetadata,character,character",
        "setTranscriptomeFromFile,UserMetadata,character,character-method",
        "setTranscriptomeFromFile,userMetadata,character,missing",
        "setTranscriptomeFromFile,UserMetadata,character,missing-method"
      ]
    },
    {
      "page": "setTranscriptomeFromObject",
      "title": "Set transcriptome_object of one UserMetadata object",
      "topics": [
        "setTranscriptomeFromObject",
        "setTranscriptomeFromObject,userMetadata,DNAStringSet,character",
        "setTranscriptomeFromObject,UserMetadata,DNAStringSet,character-method"
      ]
    },
    {
      "page": "setWorkingPath",
      "title": "`working_path` Setter",
      "topics": [
        "setWorkingPath",
        "setWorkingPath,userMetadata,character",
        "setWorkingPath,UserMetadata,character-method"
      ]
    },
    {
      "page": "UserMetadata-class",
      "title": "UserMetadata S4 class",
      "topics": [
        "UserMetadata",
        "UserMetadata-class"
      ]
    }
  ],
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      "source": "bgeecall-manual.Rmd",
      "filename": "bgeecall-manual.html",
      "title": "automatic RNA-Seq present/absent gene expression calls generation",
      "author": "Julien Wollbrett, Sara Fonseca Costa, Marc Robinson-Rechavi, Frederic Bastian",
      "engine": "knitr::rmarkdown",
      "headings": [
        "How present/absent calls are generated",
        "Bgee database",
        "Reference intergenic regions",
        "Threshold of present/absent",
        "Installation",
        "How to use the BgeeCall package",
        "Load the package",
        "Quick start",
        "Generate present/absent calls for more than one RNA-Seq library",
        "Parallized generation of present/absent calls on a cluster",
        "Reference intergenic sequences",
        "Releases of reference intergenic sequences",
        "Core reference intergenic from Bgee",
        "Community reference intergenic",
        "Your own reference intergenic",
        "<a name=\"transcript_level\"></a>Generate present/absent calls at transcript level (beta version)",
        "Tune how to use kallisto",
        "Download or reuse your own kallisto",
        "Edit kallisto quant attributes",
        "Choose between two kmer size",
        "<a name=\"run_ids\"></a>Generate calls for a subset of RNA-Seq runs",
        "Modify present/absent threshold",
        "Default pValue approach",
        "Intergenic threshold approach",
        "qValue threshold approach",
        "Run BgeeCall in quiet mode",
        "Do not rerun parts of the pipeline",
        "Ignore transcript version",
        "Generate calls with a simple arborescence of directories",
        "Change directory where calls are saved",
        "<a name=\"slurm_options\"></a>Modify slurm options",
        "Number of jobs",
        "Do not submit the jobs",
        "Modify slurm options",
        "Add modules to your environment",
        "Modify BgeeCall objects",
        "Merging multiple libraries",
        "Arguments and user file to perform the merging"
      ],
      "created": "2019-02-01 18:57:39",
      "modified": "2026-05-26 11:32:58",
      "commits": 44
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