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  "Title": "Clonal Population Identification in Single-Cell RNA-Seq Data\nusing Mitochondrial and Somatic Mutations",
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  "Description": "This package primarily identifies variants in\nmitochondrial genomes from BAM alignment files. It filters\nthese variants to remove RNA editing events then estimates\ntheir evolutionary relationship (i.e. their phylogenetic tree)\nand groups single cells into clones. It also visualizes the\nmutations and providing additional genomic context.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:35 UTC",
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      "title": "Computation of phylogenetic trees and clustering of mutations",
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      "headings": [
        "Before you begin",
        "Compute a phylogenetic tree",
        "Identify clones and assign cells to clones",
        "Parameter choice",
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      "title": "Variant Calling",
      "author": "Benjamin Story",
      "engine": "knitr::rmarkdown",
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        "Introduction",
        "Package goals",
        "Genome availability",
        "Input data",
        "Counting nucleotides from BAM files",
        "Counting function examples and explanations",
        "Calling and filtering variants",
        "Calling mutations based on an exclusionlist",
        "Calling mutations based on variants shared within a cohort",
        "Example of Exclusionlist filtering",
        "Example of Cohort filtering",
        "Session information"
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      "modified": "2021-07-20 22:47:30",
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