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  "Title": "Generation of customized protein variant databases from genomic\nvariants, splice-junctions and manual sequences",
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  "Date": "2025-07-22",
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  "Description": "ProteoDisco is an R package to facilitate proteogenomics\nstudies. It houses functions to create customized (variant)\nprotein databases based on user-submitted genomic variants,\nsplice-junctions, fusion genes and manual transcript sequences.\nThe flexible workflow can be adopted to suit a myriad of\nresearch and experimental settings.",
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      "author": "Job van Riet, Wesley van de Geer and Harmen van de Werken",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Abstract",
        "Standard ProteoDisco workflow.",
        "Logging parameters.",
        "Step 1 - Generating the ProteoDiscography",
        "Using FASTA and GTF files.",
        "Using pre-generated resources.",
        "Inspecting the initial ProteoDiscography.",
        "Step 2 - Import (somatic) variants into the ProteoDiscography.",
        "Importing SNVs/MNVs/InDels (VCF).",
        "Importing manually-curated transcript sequences from complex events.",
        "Viewing all imported ProteoDiscography records",
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        "Step 4 - Importing splicing-events to generate splicing-isoforms.",
        "(Optional) Determine proteotypic peptides.",
        "(Optional) Convert TxIDs to gene symbols.",
        "Final step - Generate output FASTA",
        "Session Information"
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