{
  "_id": "6a1afb871d7bb097a09fccf2",
  "Package": "ScreenR",
  "Type": "Package",
  "Title": "Package to Perform High Throughput Biological Screening",
  "Version": "1.15.0",
  "Date": "2022-04-01",
  "Authors@R": "c(person(\"Emanuel Michele\", \"Soda\", role = c(\"aut\", \"cre\"),\nemail = \"emanuelsoda@gmail.com\",\ncomment = c(ORICD = \"0000-0002-2301-6465\")),\nperson(\"Elena\", \"Ceccacci\", role = c(\"aut\"),\nemail = \"elena.ceccacci@ieo.it\",\ncomment = c(ORICD = \"0000-0002-2285-8994\")),\nperson(\"Saverio\", \"Minucci\", role = c(\"fnd\", \"ths\"),\nemail = \"saverio.minucci@ieo.it\",\ncomment = c(ORICD = \"0000-0001-5678-536X\")))",
  "Description": "ScreenR is a package suitable to perform hit\nidentification in loss of function High Throughput Biological\nScreenings performed using barcoded shRNA-based libraries.\nScreenR combines the computing power of software such as edgeR\nwith the simplicity of use of the Tidyverse metapackage.\nScreenR executes a pipeline able to find candidate hits from\nbarcode counts, and integrates a wide range of visualization\nmodes for each step of the analysis.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
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  "VignetteBuilder": "knitr",
  "biocViews": "Software, AssayDomain, GeneExpression",
  "BugReports": "https://github.com/EmanuelSoda/ScreenR/issues",
  "URL": "https://emanuelsoda.github.io/ScreenR/",
  "Collate": "'ScreenR-package.R' 'annotation_table.R' 'barcode_lost.R'\n'camera_method.R' 'compute_data_table.R' 'compute_metrics.R'\n'count_mapped_reads.R' 'count_table.R' 'create_object.R'\n'distribution_mapped_reads.R' 'filter_by.R' 'find_common_hit.R'\n'find_roast_hit.R' 'find_robust_zscore_hit.R'\n'find_zscore_hit.R' 'generics.R' 'mapped_reads.R'\n'normalize_data.R' 'plot_barcode_hit.R' 'plot_barcode_trend.R'\n'plot_boxplot.R' 'plot_mapped_reads.R' 'plot_mds.R'\n'plot_trend.R' 'plot_zscore_distribution.R' 'screenr-class.R'\n'zzz.R'",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:31 UTC",
  "RemoteUrl": "https://github.com/bioc/ScreenR",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:50:40 UTC",
    "User": "root"
  },
  "Author": "Emanuel Michele Soda [aut, cre] (ORICD: 0000-0002-2301-6465),\nElena Ceccacci [aut] (ORICD: 0000-0002-2285-8994),\nSaverio Minucci [fnd, ths] (ORICD: 0000-0001-5678-536X)",
  "Maintainer": "Emanuel Michele Soda <emanuelsoda@gmail.com>",
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  "_created": "2026-05-30T09:50:40.000Z",
  "_published": "2026-05-30T15:00:23.602Z",
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    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "description": "“Sometimes it is the people no one can imagine anything of who do the things no one can imagine.” \n― Alan Turing",
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    "compute_data_table",
    "compute_explained_variance",
    "compute_metrics",
    "compute_slope",
    "count_mapped_reads",
    "create_edger_obj",
    "create_screenr_object",
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    "filter_by_variance",
    "find_camera_hit",
    "find_common_hit",
    "find_roast_hit",
    "find_robust_zscore_hit",
    "find_zscore_hit",
    "get_annotation_table",
    "get_count_table",
    "get_data_table",
    "get_groups",
    "get_normalized_count_table",
    "get_replicates",
    "mapped_reads",
    "normalize_data",
    "plot_barcode_hit",
    "plot_barcode_lost",
    "plot_barcode_lost_for_gene",
    "plot_barcode_trend",
    "plot_boxplot",
    "plot_common_hit",
    "plot_explained_variance",
    "plot_mapped_reads",
    "plot_mapped_reads_distribution",
    "plot_mds",
    "plot_trend",
    "plot_zscore_distribution",
    "remove_all_zero_row",
    "set_annotation_table",
    "set_count_table",
    "set_data_table",
    "set_groups",
    "set_normalized_count_table",
    "set_replicates"
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      "title": "Table for the annotation of Barcode",
      "object": "annotation_table",
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      "class": [
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      ],
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        "Barcode",
        "Gene_ID",
        "Sequence",
        "Library"
      ],
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      "table": true,
      "tojson": true
    },
    {
      "name": "count_table",
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      "object": "count_table",
      "file": "count_table.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Barcode",
        "Time_1",
        "Time_2",
        "Time_3_TRT_rep1",
        "Time_3_TRT_rep2",
        "Time_3_TRT_rep3",
        "Time_3_rep1",
        "Time_3_rep2",
        "Time_3_rep3",
        "Time_4_TRT_rep1",
        "Time_4_TRT_rep2",
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  "_help": [
    {
      "page": "annotation_table",
      "title": "Table for the annotation of Barcode",
      "concept": [
        "data"
      ],
      "topics": [
        "annotation_table"
      ]
    },
    {
      "page": "barcode_lost",
      "title": "Count number of barcode lost",
      "concept": [
        "compute"
      ],
      "topics": [
        "barcode_lost"
      ]
    },
    {
      "page": "compute_data_table",
      "title": "Compute data Table",
      "concept": [
        "compute"
      ],
      "topics": [
        "compute_data_table"
      ]
    },
    {
      "page": "compute_metrics",
      "title": "Compute Metrics",
      "concept": [
        "compute"
      ],
      "topics": [
        "compute_metrics"
      ]
    },
    {
      "page": "compute_slope",
      "title": "Compute Slope of a Gene",
      "concept": [
        "compute"
      ],
      "topics": [
        "compute_slope"
      ]
    },
    {
      "page": "count_mapped_reads",
      "title": "Count the number of mapped read",
      "concept": [
        "compute"
      ],
      "topics": [
        "count_mapped_reads"
      ]
    },
    {
      "page": "count_table",
      "title": "Table of the count table",
      "concept": [
        "data"
      ],
      "topics": [
        "count_table"
      ]
    },
    {
      "page": "create_edger_obj",
      "title": "Create edgeR Object",
      "concept": [
        "objects"
      ],
      "topics": [
        "create_edger_obj"
      ]
    },
    {
      "page": "create_screenr_object",
      "title": "Create the ScreenR Object",
      "concept": [
        "objects"
      ],
      "topics": [
        "create_screenr_object"
      ]
    },
    {
      "page": "filter_by_slope",
      "title": "Filter using the slope filter",
      "concept": [
        "filter"
      ],
      "topics": [
        "filter_by_slope"
      ]
    },
    {
      "page": "filter_by_variance",
      "title": "Filter using the variance filter",
      "concept": [
        "filter"
      ],
      "topics": [
        "filter_by_variance"
      ]
    },
    {
      "page": "find_camera_hit",
      "title": "Find Camera Hit",
      "concept": [
        "find"
      ],
      "topics": [
        "find_camera_hit"
      ]
    },
    {
      "page": "find_common_hit",
      "title": "Find common hit",
      "concept": [
        "find"
      ],
      "topics": [
        "find_common_hit"
      ]
    },
    {
      "page": "find_roast_hit",
      "title": "Find Roast Hit",
      "concept": [
        "find"
      ],
      "topics": [
        "find_roast_hit"
      ]
    },
    {
      "page": "find_robust_zscore_hit",
      "title": "Title Find robust Z-score Hit",
      "concept": [
        "find"
      ],
      "topics": [
        "find_robust_zscore_hit"
      ]
    },
    {
      "page": "find_zscore_hit",
      "title": "Title Find Z-score Hit",
      "concept": [
        "find"
      ],
      "topics": [
        "find_zscore_hit"
      ]
    },
    {
      "page": "get_annotation_table",
      "title": "Get ScreenR annotation table",
      "concept": [
        "objects"
      ],
      "topics": [
        "get_annotation_table",
        "get_annotation_table,screenr_object",
        "get_annotation_table,screenr_object-method"
      ]
    },
    {
      "page": "get_count_table",
      "title": "Get ScreenR count table",
      "concept": [
        "objects"
      ],
      "topics": [
        "get_count_table",
        "get_count_table,screenr_object",
        "get_count_table,screenr_object-method",
        "screenr_object",
        "screenr_object-class"
      ]
    },
    {
      "page": "get_data_table",
      "title": "Get ScreenR data_table",
      "concept": [
        "objects"
      ],
      "topics": [
        "get_data_table",
        "get_data_table,screenr_object",
        "get_data_table,screenr_object-method"
      ]
    },
    {
      "page": "get_groups",
      "title": "Get ScreenR groups",
      "concept": [
        "objects"
      ],
      "topics": [
        "get_groups",
        "get_groups,screenr_object",
        "get_groups,screenr_object-method"
      ]
    },
    {
      "page": "get_normalized_count_table",
      "title": "Get ScreenR normalized_count_table",
      "concept": [
        "objects"
      ],
      "topics": [
        "get_normalized_count_table",
        "get_normalized_count_table,screenr_object",
        "get_normalized_count_table,screenr_object-method"
      ]
    },
    {
      "page": "get_replicates",
      "title": "Get ScreenR replicates",
      "concept": [
        "objects"
      ],
      "topics": [
        "get_replicates",
        "get_replicates,screenr_object",
        "get_replicates,screenr_object-method"
      ]
    },
    {
      "page": "mapped_reads",
      "title": "Mapped Reads",
      "concept": [
        "compute"
      ],
      "topics": [
        "mapped_reads"
      ]
    },
    {
      "page": "normalize_data",
      "title": "Normalize data",
      "concept": [
        "compute"
      ],
      "topics": [
        "normalize_data"
      ]
    },
    {
      "page": "plot_barcode_hit",
      "title": "Plot barcode hit",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_barcode_hit"
      ]
    },
    {
      "page": "plot_barcode_lost",
      "title": "Plot number of barcode lost",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_barcode_lost"
      ]
    },
    {
      "page": "plot_barcode_lost_for_gene",
      "title": "Plot number of barcode lost for gene",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_barcode_lost_for_gene"
      ]
    },
    {
      "page": "plot_barcode_trend",
      "title": "Plot the trend over time of the barcodes",
      "topics": [
        "plot_barcode_trend"
      ]
    },
    {
      "page": "plot_boxplot",
      "title": "Plot Barcodes Hit",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_boxplot"
      ]
    },
    {
      "page": "plot_common_hit",
      "title": "Plot common hit",
      "topics": [
        "plot_common_hit"
      ]
    },
    {
      "page": "plot_explained_variance",
      "title": "Plot the explained variance by the PC",
      "topics": [
        "plot_explained_variance"
      ]
    },
    {
      "page": "plot_mapped_reads",
      "title": "Plot mapped reads",
      "topics": [
        "plot_mapped_reads"
      ]
    },
    {
      "page": "plot_mapped_reads_distribution",
      "title": "Plot the distribution of the mapped reads",
      "concept": [
        "plot"
      ],
      "topics": [
        "plot_mapped_reads_distribution"
      ]
    },
    {
      "page": "plot_mds",
      "title": "Multidimensional Scaling Plot",
      "topics": [
        "plot_mds"
      ]
    },
    {
      "page": "plot_trend",
      "title": "Plot the trend hit gene",
      "topics": [
        "plot_trend"
      ]
    },
    {
      "page": "plot_zscore_distribution",
      "title": "Plot distribution Z-score",
      "topics": [
        "plot_zscore_distribution"
      ]
    },
    {
      "page": "remove_all_zero_row",
      "title": "Remove rows that have zero count in all samples",
      "concept": [
        "compute"
      ],
      "topics": [
        "remove_all_zero_row"
      ]
    },
    {
      "page": "set_annotation_table",
      "title": "Set ScreenR annotation table",
      "concept": [
        "objects"
      ],
      "topics": [
        "set_annotation_table",
        "set_annotation_table,screenr_object",
        "set_annotation_table,screenr_object-method"
      ]
    },
    {
      "page": "set_count_table",
      "title": "Set ScreenR count table",
      "concept": [
        "objects"
      ],
      "topics": [
        "set_count_table",
        "set_count_table,screenr_object",
        "set_count_table,screenr_object-method"
      ]
    },
    {
      "page": "set_data_table",
      "title": "Set ScreenR data_table",
      "concept": [
        "objects"
      ],
      "topics": [
        "set_data_table",
        "set_data_table,screenr_object",
        "set_data_table,screenr_object-method"
      ]
    },
    {
      "page": "set_groups",
      "title": "Set ScreenR groups",
      "concept": [
        "objects"
      ],
      "topics": [
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