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  "Package": "ECLIPSE",
  "Title": "Enhanced CLonotypic Inference via Prediction of Single-cell\nExpression",
  "Version": "0.99.3",
  "Authors@R": "c(\nperson(\"Ethan\", \"Burns\", comment = c(ORCID = \"0009-0009-8061-3686\"), email = \"ethan.burns@yale.edu\", role = c(\"aut\", \"cre\")),\nperson(\"Zhaochen\", \"Ye\", comment = c(ORCID = \"0009-0000-4422-3861\"), email = \"zhaochen.ye@yale.edu\", role = \"ctb\"),\nperson(\"Kelly\", \"Street\", comment = c(ORCID = \"0000-0001-6379-5013\"), email = \"kelly.street@gmail.com\", role = \"ctb\"),\nperson(\"David\", \"Braun\", comment = c(ORCID = \"0000-0003-4543-5553\"), email = \"david.braun@yale.edu\", role = c(\"aut\", \"fnd\")))",
  "Description": "This package is used for the analysis of single-cell T\ncell receptor sequencing data (scTCR-seq). ECLIPSE maps chain\npairings across a sample to predict the true clonotype of each\ncell, unlike other methods which only consider the chains that\nare sequenced in each cell. Seurat/SingleCellExperiment objects\nand Cell Ranger vdj/multi contig files are required as inputs.",
  "License": "GPL (>= 3)",
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  "biocViews": "Software, GeneExpression, BiomedicalInformatics,\nImmunoOncology, Transcriptomics, Classification, SingleCell,\nAnnotation, Sequencing",
  "BugReports": "https://github.com/eburns10/ECLIPSE/issues",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-11-10 20:57:59 UTC",
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  "Author": "Ethan Burns [aut, cre] (ORCID: <https://orcid.org/0009-0009-8061-3686>),\nZhaochen Ye [ctb] (ORCID: <https://orcid.org/0009-0000-4422-3861>),\nKelly Street [ctb] (ORCID: <https://orcid.org/0000-0001-6379-5013>),\nDavid Braun [aut, fnd] (ORCID: <https://orcid.org/0000-0003-4543-5553>)",
  "Maintainer": "Ethan Burns <ethan.burns@yale.edu>",
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  "_type": "src",
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      "title": "Example Post-QC TCR contigs that would be generated within ECLIPSE and passed to findThreeChainClones.",
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      "page": "dot-assignFinalClonotypes",
      "title": "Assign final clonotypes",
      "topics": [
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      ]
    },
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      "page": "dot-findMissingMonotypicChains",
      "title": "Find missing monotypic chains",
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      ]
    },
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      "page": "dot-identifyThreeChainClones",
      "title": "Identify three TCR chain clones",
      "topics": [
        ".identifyThreeChainClones"
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    },
    {
      "page": "dot-modifyThreeChainContigs",
      "title": "Modify three TCR chain contigs",
      "topics": [
        ".modifyThreeChainContigs"
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    },
    {
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      "title": "QC filter contigs",
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    {
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      "title": "Read TCR contigs",
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      "title": "Reformat Seurat object",
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      "title": "Run VDJdive",
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    {
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      "topics": [
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    },
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      "title": "Introduction to ECLIPSE",
      "author": "Ethan C. Burns, David A. Braun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "What is ECLIPSE? Why should I use it to analyze my scTCR-seq data?",
        "What are the inputs to ECLIPSE? Is there any pre-processing required?",
        "How is ECLIPSE different from other Bioconductor and non-Bioconductor scTCR-seq analysis packages?",
        "Installation and loading",
        "Test dataset",
        "Preparing inputs for ECLIPSE",
        "Contig files",
        "Option 1: use folder paths",
        "Option 2: use contig file paths",
        "Seurat object meta.data",
        "Column to pass to original_barcode",
        "Column to pass to batch",
        "Column to pass to donor",
        "Column to pass to group",
        "Running the ECLIPSE function",
        "Description of function",
        "Running ECLIPSE",
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        "Conclusions",
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        "Using ECLIPSE without a Seurat object",
        "SingleCellExperiment objects",
        "Other objects",
        "Helper function: findThreeChainClones",
        "ECLIPSE additional arguments",
        "Seurat object columns description",
        "Session info"
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      "modified": "2026-11-10 20:57:59",
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