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  "Description": "Analysis of minor alleles in Illumina sequencing data of\nviral genomes. Functions in 'vivaldi' primarily operate on vcf\nfiles.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/GreshamLab/vivaldi",
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    "filter_variants",
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    "position_allele_freq",
    "prepare_annotations",
    "read_reference_fasta_dna",
    "shannon_entropy",
    "shared_snv_plot",
    "shared_snv_table",
    "snpeff_info",
    "snv_genome",
    "snv_location",
    "snv_segment",
    "tally_it",
    "tstv_plot",
    "tstv_ratio"
  ],
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      "name": "example_filtered_SNV_df",
      "title": "Example Dataframe The DF_filt_SNVs dataframe created in the vignette",
      "object": "example_filtered_SNV_df",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "sample",
        "POS",
        "REF",
        "ALT",
        "allele",
        "annotation",
        "putative_impact",
        "gene_name",
        "gene_id",
        "feature_type",
        "feature_id",
        "transcript_biotype",
        "rank_total",
        "HGVS.c",
        "HGVS.p",
        "cDNA_position",
        "CDS_position",
        "protein_position",
        "distance_to_feature",
        "errors",
        "ALT_TYPE",
        "major",
        "minor",
        "filename.x",
        "replicate.x",
        "gt_DP.x",
        "REF_COUNT.x",
        "ALT_COUNT.x",
        "REF_FREQ.x",
        "ALT_FREQ.x",
        "majorcount.x",
        "minorcount.x",
        "majorfreq.x",
        "minorfreq.x",
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        "replicate.y",
        "gt_DP.y",
        "REF_COUNT.y",
        "ALT_COUNT.y",
        "REF_FREQ.y",
        "ALT_FREQ.y",
        "majorcount.y",
        "minorcount.y",
        "majorfreq.y",
        "minorfreq.y",
        "minorfreq",
        "majorfreq",
        "weighted_minorfreq",
        "weighted_majorfreq",
        "SegmentSize",
        "STRAIN",
        "shannon_ntpos",
        "chrom_shannon",
        "genome_shannon",
        "shannon_chrom_perkb",
        "genome_shannon_perkb"
      ],
      "rows": 735,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
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      "page": "add_metadata",
      "title": "add_metadata",
      "topics": [
        "add_metadata"
      ]
    },
    {
      "page": "af_distribution",
      "title": "af_distribution",
      "topics": [
        "af_distribution"
      ]
    },
    {
      "page": "arrange_data",
      "title": "arrange_data",
      "topics": [
        "arrange_data"
      ]
    },
    {
      "page": "dNdS_segment",
      "title": "dNdS_segment",
      "topics": [
        "dNdS_segment"
      ]
    },
    {
      "page": "example_filtered_SNV_df",
      "title": "Example Dataframe The DF_filt_SNVs dataframe created in the vignette",
      "topics": [
        "example_filtered_SNV_df"
      ]
    },
    {
      "page": "filter_variants",
      "title": "filter_variants",
      "topics": [
        "filter_variants"
      ]
    },
    {
      "page": "merge_replicates",
      "title": "merge_replicates",
      "topics": [
        "merge_replicates"
      ]
    },
    {
      "page": "plot_shannon",
      "title": "plot_shannon",
      "topics": [
        "plot_shannon"
      ]
    },
    {
      "page": "position_allele_freq",
      "title": "position_allele_freq",
      "topics": [
        "position_allele_freq"
      ]
    },
    {
      "page": "prepare_annotations",
      "title": "prepare_annotations",
      "topics": [
        "prepare_annotations"
      ]
    },
    {
      "page": "read_reference_fasta_dna",
      "title": "read_reference_fasta_dna",
      "topics": [
        "read_reference_fasta_dna"
      ]
    },
    {
      "page": "shannon_entropy",
      "title": "shannon_entropy",
      "topics": [
        "shannon_entropy"
      ]
    },
    {
      "page": "shared_snv_plot",
      "title": "shared_snv_plot",
      "topics": [
        "shared_snv_plot"
      ]
    },
    {
      "page": "shared_snv_table",
      "title": "shared_snv_table",
      "topics": [
        "shared_snv_table"
      ]
    },
    {
      "page": "snpeff_info",
      "title": "snpeff_info",
      "topics": [
        "snpeff_info"
      ]
    },
    {
      "page": "snv_genome",
      "title": "snv_genome",
      "topics": [
        "snv_genome"
      ]
    },
    {
      "page": "snv_location",
      "title": "snv_location",
      "topics": [
        "snv_location"
      ]
    },
    {
      "page": "snv_segment",
      "title": "snv_segment",
      "topics": [
        "snv_segment"
      ]
    },
    {
      "page": "tally_it",
      "title": "tally_it",
      "topics": [
        "tally_it"
      ]
    },
    {
      "page": "tstv_plot",
      "title": "tstv_plot",
      "topics": [
        "tstv_plot"
      ]
    },
    {
      "page": "tstv_ratio",
      "title": "tstv_ratio",
      "topics": [
        "tstv_ratio"
      ]
    }
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      "engine": "knitr::rmarkdown",
      "headings": [
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        "Vignette data set",
        "Step 1: Set path for variant data and metadata",
        "Step 2: Loading data and arranging",
        "Load VCF files into a dataframe",
        "Merging Replicate Sequence Data",
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        "Compare the similarity between the average allele frequency and the weighted average allele frequency",
        "Filter out variants based on coverage and/or frequency cutoffs",
        "Format SNPeff information",
        "Remove duplicate variants in NS and MP",
        "Add metadata",
        "Step 3: Calculations and Visualization",
        "Plot distribution of all minor variant frequencies",
        "Count number of SNVs",
        "Plot location of SNVs across segments",
        "Plot number of SNVs per sample and per segment",
        "Calculate Transition/Transversion Ratio",
        "Plot TsTv",
        "Calculate Shannon entropy",
        "Plot shannon entropy per sample and per segment",
        "Calculate dNdS ratio and plot per sample per protein product",
        "Identify variants shared among samples",
        "Print dataframe of variants shared among samples for further analysis",
        "Isolate variant of interest and plot AF at that position in all samples"
      ],
      "created": "2022-10-07 21:54:24",
      "modified": "2023-03-02 21:52:43",
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