{
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  "Type": "Package",
  "Title": "Automatic RNA-Seq present/absent gene expression calls\ngeneration",
  "Version": "1.29.3",
  "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",
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  "Date/Publication": "2026-07-03 08:24:50 UTC",
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      {
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        "hash": "1ddf6c5976ed4adf"
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      {
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      {
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      },
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      },
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        "hash": "3298b032f799ff5f"
      },
      {
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        "hash": "5b9ffd1b7c0904ea"
      },
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        "hash": "d3c9336234ee1090"
      },
      {
        "key": "BgeeCall::generic:setRunIds",
        "hash": "30a7265a44656818"
      },
      {
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        "hash": "d9bb7df6809e3fa2"
      },
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        "key": "BgeeCall::generic:setTranscriptomeFromFile",
        "hash": "8d7084ce64845854"
      },
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        "hash": "a7ed127b51a0f8e2"
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      }
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    "extra/citation.html",
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    "extra/contents.json",
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    "extra/readme.md",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/bgeedb/bgeecall",
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  "_cranurl": false,
  "_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"
  ],
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      "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"
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    },
    {
      "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": [
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