{
  "_id": "6a489cd1e06c18f0a6543308",
  "Package": "ddpcr",
  "Title": "Analysis and Visualization of Droplet Digital PCR in R and on\nthe Web",
  "Version": "1.16.0",
  "Authors@R": "c(\nperson(\"Dean\", \"Attali\", email = \"daattali@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment= c(ORCID=\"0000-0002-5645-3493\"))\n)",
  "Description": "An interface to explore, analyze, and visualize droplet\ndigital PCR (ddPCR) data in R. This is the first\nnon-proprietary software for analyzing two-channel ddPCR data.\nAn interactive tool was also created and is available online to\nfacilitate this analysis for anyone who is not comfortable with\nusing R.",
  "URL": "https://github.com/daattali/ddpcr,\nhttps://daattali.com/shiny/ddpcr/",
  "BugReports": "https://github.com/daattali/ddpcr/issues",
  "License": "MIT + file LICENSE",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.3",
  "Encoding": "UTF-8",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nlibx11-dev zlib1g-dev",
  "Repository": "https://daattali.r-universe.dev",
  "Date/Publication": "2026-01-14 07:15:39 UTC",
  "RemoteUrl": "https://github.com/daattali/ddpcr",
  "RemoteRef": "HEAD",
  "RemoteSha": "92acedb3eb8f9fe81b50661f111720a63a4f1551",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 05:26:32 UTC",
    "User": "root"
  },
  "Author": "Dean Attali [aut, cre] (ORCID: <https://orcid.org/0000-0002-5645-3493>)",
  "Maintainer": "Dean Attali <daattali@gmail.com>",
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  "_created": "2026-07-04T05:26:32.000Z",
  "_published": "2026-07-04T05:40:33.589Z",
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  "_exports": [
    "%>%",
    "%btwn%",
    "analysis_complete",
    "analyze",
    "bind_df_ends",
    "calc_negative_freq_simple",
    "calculate_concentration",
    "calculate_concentration_single",
    "calculate_neg_freq_single",
    "calculate_negative_freqs",
    "capitalize",
    "cat0",
    "check_step",
    "classify_droplets",
    "classify_droplets_single",
    "classify_thresholds",
    "cluster",
    "cluster_name",
    "clusters",
    "col_to_num",
    "define_clusters",
    "define_params",
    "define_steps",
    "err_msg",
    "get_col",
    "get_empty_cutoff",
    "get_filled_border",
    "get_filled_drops",
    "get_outlier_cutoff",
    "get_row",
    "get_single_well",
    "get_wells_btwn",
    "has_signif_negative_cluster",
    "has_step",
    "is_dir",
    "is_dirty",
    "is_empty_plate",
    "is_file",
    "is_range",
    "is_well_success",
    "launch",
    "load_plate",
    "local_maxima",
    "local_minima",
    "lol_to_df",
    "mark_clusters",
    "merge_dfs_overwrite_col",
    "meta_var_name",
    "move_back",
    "move_front",
    "msg",
    "name",
    "name<-",
    "named_vec_to_df",
    "negative_name",
    "negative_name<-",
    "new_plate",
    "next_step",
    "normalize_to_rds",
    "num_to_col",
    "num_to_row",
    "other_dim",
    "params",
    "params<-",
    "parent_plate_type",
    "plate_data",
    "plate_data<-",
    "plate_meta",
    "plate_meta<-",
    "plate_types",
    "point2d",
    "positive_dim",
    "positive_dim_var",
    "positive_dim<-",
    "positive_name",
    "positive_name<-",
    "quiet",
    "range_list_to_vec",
    "range_to_endpoints",
    "range_to_seq",
    "reclassify_droplets",
    "reclassify_droplets_single",
    "remove_empty",
    "remove_failures",
    "remove_outliers",
    "reset",
    "row_to_num",
    "sample_data_dir",
    "sample_data_file",
    "sample_plate",
    "sample_results_file",
    "save_plate",
    "set_default_params",
    "set_thresholds",
    "status",
    "status<-",
    "step",
    "step_begin",
    "step_end",
    "step_name",
    "steps",
    "thresholds",
    "thresholds<-",
    "type",
    "unanalyzed_clusters",
    "variable_dim",
    "variable_dim_var",
    "variable_dim<-",
    "warn_msg",
    "WELL_ID_REGEX",
    "well_info",
    "wells_failed",
    "wells_mutant",
    "wells_negative",
    "wells_positive",
    "wells_success",
    "wells_used",
    "wells_wildtype",
    "x_threshold",
    "x_threshold<-",
    "x_var",
    "x_var<-",
    "y_threshold",
    "y_threshold<-",
    "y_var",
    "y_var<-"
  ],
  "_help": [
    {
      "page": "analysis_complete",
      "title": "Is the analysis complete?",
      "topics": [
        "analysis_complete"
      ]
    },
    {
      "page": "analyze",
      "title": "Run analysis on a ddPCR plate",
      "topics": [
        "analyze"
      ]
    },
    {
      "page": "clusters",
      "title": "Potential droplet clusters for a plate type",
      "topics": [
        "clusters"
      ]
    },
    {
      "page": "custom_thresholds",
      "title": "Plate type: custom thresholds",
      "topics": [
        "custom_thresholds"
      ]
    },
    {
      "page": "ddpcr_plate",
      "title": "Plate type: ddPCR plate",
      "topics": [
        "ddpcr_plate"
      ]
    },
    {
      "page": "fam_positive_pnpp",
      "title": "Plate type: FAM-positive PNPP",
      "topics": [
        "fam_positive_pnpp"
      ]
    },
    {
      "page": "hex_positive_pnpp",
      "title": "Plate type: HEX-positive PNPP",
      "topics": [
        "hex_positive_pnpp"
      ]
    },
    {
      "page": "launch",
      "title": "Run the interactive analysis tool (Shiny app) in a web browser",
      "topics": [
        "launch"
      ]
    },
    {
      "page": "load_plate",
      "title": "Load a previously saved ddPCR plate",
      "topics": [
        "load_plate"
      ]
    },
    {
      "page": "name",
      "title": "Plate name",
      "topics": [
        "name",
        "name<-"
      ]
    },
    {
      "page": "new_plate",
      "title": "Create a new ddPCR plate",
      "topics": [
        "new_plate"
      ]
    },
    {
      "page": "next_step",
      "title": "Run the next step in an analysis",
      "topics": [
        "next_step"
      ]
    },
    {
      "page": "params",
      "title": "Plate parameters",
      "topics": [
        "params",
        "params<-"
      ]
    },
    {
      "page": "plate_data",
      "title": "Plate data (droplets data)",
      "topics": [
        "plate_data"
      ]
    },
    {
      "page": "plate_meta",
      "title": "Plate metadata",
      "topics": [
        "plate_meta"
      ]
    },
    {
      "page": "plate_types",
      "title": "Supported plate types",
      "topics": [
        "plate_types"
      ]
    },
    {
      "page": "plot.custom_thresholds",
      "title": "Plot a ddPCR plate of type custom thresholds",
      "topics": [
        "plot.custom_thresholds"
      ]
    },
    {
      "page": "plot.ddpcr_plate",
      "title": "Plot a ddPCR plate",
      "topics": [
        "plot.ddpcr_plate"
      ]
    },
    {
      "page": "plot.wildtype_mutant_pnpp",
      "title": "Plot a ddPCR plate of type wildtype/mutant PNPP",
      "topics": [
        "plot.wildtype_mutant_pnpp"
      ]
    },
    {
      "page": "pnpp_experiment",
      "title": "Plate type: PNPP experiment",
      "topics": [
        "pnpp_experiment"
      ]
    },
    {
      "page": "reset",
      "title": "Reset a plate",
      "topics": [
        "reset"
      ]
    },
    {
      "page": "sample_data",
      "title": "Get sample data",
      "topics": [
        "sample_data",
        "sample_data_dir",
        "sample_data_file",
        "sample_plate",
        "sample_results_file"
      ]
    },
    {
      "page": "save_plate",
      "title": "Save a ddPCR plate",
      "topics": [
        "save_plate"
      ]
    },
    {
      "page": "set_default_params",
      "title": "Reset plate parameters to their defaults",
      "topics": [
        "set_default_params"
      ]
    },
    {
      "page": "steps",
      "title": "Analysis steps of a ddPCR plate",
      "topics": [
        "steps"
      ]
    },
    {
      "page": "subset.ddpcr_plate",
      "title": "Subsetting a ddPCR plate",
      "topics": [
        "subset.ddpcr_plate"
      ]
    },
    {
      "page": "thresholds",
      "title": "Get/set the thresholds",
      "topics": [
        "set_thresholds",
        "thresholds",
        "thresholds<-"
      ]
    },
    {
      "page": "type",
      "title": "Plate type",
      "topics": [
        "type"
      ]
    },
    {
      "page": "well_info",
      "title": "Get metadata info of a well",
      "topics": [
        "well_info"
      ]
    },
    {
      "page": "wells_mutant",
      "title": "Get mutant wells",
      "topics": [
        "wells_mutant"
      ]
    },
    {
      "page": "wells_negative",
      "title": "Get negative wells",
      "topics": [
        "wells_negative"
      ]
    },
    {
      "page": "wells_positive",
      "title": "Get positive wells",
      "topics": [
        "wells_positive"
      ]
    },
    {
      "page": "wells_success",
      "title": "Get successful/failed wells",
      "topics": [
        "wells_failed",
        "wells_success"
      ]
    },
    {
      "page": "wells_used",
      "title": "Get wells used in a ddPCR plate",
      "topics": [
        "wells_used"
      ]
    },
    {
      "page": "wells_wildtype",
      "title": "Get wildtype wells",
      "topics": [
        "wells_wildtype"
      ]
    },
    {
      "page": "wildtype_mutant_pnpp",
      "title": "Plate type: wildtype/mutant PNPP",
      "topics": [
        "wildtype_mutant_pnpp"
      ]
    },
    {
      "page": "x_threshold",
      "title": "Get/set the X threshold",
      "topics": [
        "x_threshold",
        "x_threshold<-"
      ]
    },
    {
      "page": "x_var",
      "title": "Get/set the X/Y variable (dye name)",
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        "x_var",
        "x_var<-",
        "y_var",
        "y_var<-"
      ]
    },
    {
      "page": "y_threshold",
      "title": "Get/set the Y threshold",
      "topics": [
        "y_threshold",
        "y_threshold<-"
      ]
    }
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  "_vignettes": [
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      "source": "algorithm.Rmd",
      "filename": "algorithm.html",
      "title": "Algorithms in ddpcr analysis",
      "author": "Dean Attali",
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      "headings": [
        "Algorithms used to analyze ddPCR droplets",
        "Step 1: Identify failed wells",
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        "Step 3: Identify empty droplets",
        "Step 4: Gate droplets",
        "Step 4.1: Identify rain droplets",
        "Step 4.2: Identify mutant versus wildtype droplets",
        "Step 4.3: Classify wells as mutant versus wildtype",
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      "title": "Extending ddpcr by adding new plate types",
      "author": "Dean Attali",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Extending ddpcr by adding new plate types",
        "Default plate type: ddpcr_plate",
        "Built-in plate types",
        "Functions to implement when adding a new plate type",
        "parent_plate_type(): Define parent plate type",
        "define_params(): Define plate type parameters",
        "define_clusters(): Define droplet clusters",
        "define_steps(): Define analysis steps",
        "Changing the algorithm of an existing step",
        "plot(): Plot a ddPCR plate",
        "Example"
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        "A plate object is a list",
        "Using S3 for plate objects to override base generic functions",
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        "Analysis of different built-in plate types",
        "How the analysis steps work"
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      "title": "Package ddpcr",
      "author": "Dean Attali",
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      "headings": [
        "ddpcr: Analysis and visualization of Droplet Digital PCR data in R and on the web",
        "Table of contents"
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      "modified": "2026-01-14 06:40:59",
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