{
  "_id": "6a1aedc61d7bb097a09f53e5",
  "Package": "TSAR",
  "Type": "Package",
  "Title": "Thermal Shift Analysis in R",
  "Version": "1.11.0",
  "Year": "2025",
  "Authors@R": "c(person(\"Xinlin\", \n\"Gao\",\nemail = \"candygao2015@outlook.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0002-2518-235X\")),\nperson(c(\"William\", \"M.\"),\n\"McFadden\",\nemail = \"wmm27@pitt.edu\",\nrole = c(\"aut\",\"fnd\"),\ncomment = c(ORCID = \"0000-0001-6911-2172\")),\nperson(c(\"Zhijiang\", \"Ye\"),\n\"Ye\",\nemail = \"zhijiang.ye@emory.edu\",\nrole = c(\"aut\",\"fnd\"),\ncomment = c(ORCID = \"0009-0005-5464-7306\")),\nperson(c(\"Stefan\", \"G.\"),\n\"Sarafianos\",\nemail = \"stefanos.sarafianos@emory.edu\",\nrole = c(\"fnd\",\"aut\",\"ths\"),\ncomment = c(ORCID = \"0000-0002-5840-154X\"))\n)",
  "Description": "This package automates analysis workflow for Thermal Shift\nAnalysis (TSA) data. Processing, analyzing, and visualizing\ndata through both shiny applications and command lines. Package\naims to simplify data analysis and offer front to end workflow,\nfrom raw data to multiple trial analysis.",
  "License": "AGPL-3",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "Testthat": "true",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "biocViews": "Software, ShinyApps, Visualization, qPCR",
  "DataRaw": "data/qPCR_data1.rda",
  "DataRaw2": "data/qPCR_data2.rda",
  "DataRaw3": "data/Well_Information.rda",
  "DataRaw4": "data/Well_Information_Template.rda",
  "DataRawr": "data/example_tsar_data.rda",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libssl-dev\nzlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:34 UTC",
  "RemoteUrl": "https://github.com/bioc/TSAR",
  "RemoteRef": "HEAD",
  "RemoteSha": "5ead14fb1d7adc82acd0ea84b450c0ae6888df2f",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 09:41:19 UTC",
    "User": "root"
  },
  "Author": "Xinlin Gao [aut, cre] (ORCID: <https://orcid.org/0009-0002-2518-235X>),\nWilliam M. McFadden [aut, fnd] (ORCID:\n<https://orcid.org/0000-0001-6911-2172>),\nZhijiang Ye Ye [aut, fnd] (ORCID:\n<https://orcid.org/0009-0005-5464-7306>),\nStefan G. Sarafianos [fnd, aut, ths] (ORCID:\n<https://orcid.org/0000-0002-5840-154X>)",
  "Maintainer": "Xinlin Gao <candygao2015@outlook.com>",
  "MD5sum": "1994663b30e1223c8fabe889bd1e237b",
  "_user": "bioc",
  "_type": "src",
  "_file": "TSAR_1.11.0.tar.gz",
  "_fileid": "c280c9a730951e471cafa7d8726df1868807fa36d86f906cd65568b5fd5b7b6a",
  "_filesize": 7904597,
  "_sha256": "c280c9a730951e471cafa7d8726df1868807fa36d86f906cd65568b5fd5b7b6a",
  "_created": "2026-05-30T09:41:19.000Z",
  "_published": "2026-05-30T14:01:42.206Z",
  "_jobs": [
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  "_bioccheck": {
    "error": 2,
    "warning": 3,
    "note": 13
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676474959",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/TSAR",
  "_commit": {
    "id": "5ead14fb1d7adc82acd0ea84b450c0ae6888df2f",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381294
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  "_maintainer": {
    "name": "Xinlin Gao",
    "email": "candygao2015@outlook.com",
    "login": "cgao123",
    "uuid": 46572407
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.0.7",
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      "package": "ggplot2",
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2025-45",
      "n": 1
    },
    {
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  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.11.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.10.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "shinyapps",
    "visualization",
    "qpcr"
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 258,
    "source": "https://www.bioconductor.org/packages/stats/bioc/TSAR"
  },
  "_searchresults": 14,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/TSAR.html",
    "manual.pdf"
  ],
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "analyze_norm",
    "condition_IDs",
    "gam_analysis",
    "get_legend",
    "graph_tsar",
    "join_well_info",
    "merge_norm",
    "merge_TSA",
    "model_beta",
    "model_boltzmann",
    "model_fit",
    "model_gam",
    "normalize",
    "normalize_fluorescence",
    "read_analysis",
    "read_raw_data",
    "read_tsar",
    "remove_raw",
    "rescale",
    "run_boltzmann",
    "screen",
    "Tm_difference",
    "Tm_est",
    "TSA_average",
    "TSA_boxplot",
    "TSA_compare_plot",
    "TSA_ligands",
    "TSA_proteins",
    "TSA_Tms",
    "TSA_wells_plot",
    "view_deriv",
    "view_model",
    "weed_raw",
    "well_IDs",
    "write_tsar"
  ],
  "_datasets": [
    {
      "name": "example_normalized_data",
      "title": "Example normalized TSA dataset",
      "object": "example_normalized_data",
      "file": "example_normalized_data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "well_ID",
        "Well",
        "Protein",
        "Ligand",
        "Tm",
        "dTm D",
        "Analysis Group",
        "Flags",
        "Experiment File Name",
        "condition_ID",
        "Well.Position",
        "Temperature",
        "Fluorescence",
        "RFU"
      ],
      "rows": 63544,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_tsar_data",
      "title": "Example tsar_data file",
      "object": "example_tsar_data",
      "file": "example_tsar_data.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Well",
        "Temperature",
        "Fluorescence",
        "Normalized",
        "norm_deriv",
        "Tm",
        "Protein",
        "Ligand",
        "ExperimentFileName",
        "well_ID",
        "condition_ID"
      ],
      "rows": 28290,
      "table": true,
      "tojson": true
    },
    {
      "name": "qPCR_data1",
      "title": "qPCR_data1 Dataset",
      "object": "qPCR_data1",
      "file": "qPCR_data1.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Well",
        "Well.Position",
        "Reading",
        "Temperature",
        "Fluorescence"
      ],
      "rows": 29544,
      "table": true,
      "tojson": true
    },
    {
      "name": "qPCR_data2",
      "title": "qPCR_data2 Dataset",
      "object": "qPCR_data2",
      "file": "qPCR_data2.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Well",
        "Well.Position",
        "Reading",
        "Temperature",
        "Fluorescence"
      ],
      "rows": 29544,
      "table": true,
      "tojson": true
    },
    {
      "name": "well_information",
      "title": "example well information Data",
      "object": "well_information",
      "file": "well_information.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "...1",
        "Protein...2",
        "Ligand...3",
        "Protein...4",
        "Ligand...5",
        "Protein...6",
        "Ligand...7",
        "Protein...8",
        "Ligand...9",
        "Protein...10",
        "Ligand...11",
        "Protein...12",
        "Ligand...13",
        "Protein...14",
        "Ligand...15",
        "Protein...16",
        "Ligand...17",
        "Protein...18",
        "Ligand...19",
        "Protein...20",
        "Ligand...21",
        "Protein...22",
        "Ligand...23",
        "Protein...24",
        "Ligand...25"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    },
    {
      "name": "well_information_template",
      "title": "Well Information Template",
      "object": "well_information_template",
      "file": "well_information_template.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "...1",
        "Protein...2",
        "Ligand...3",
        "Protein...4",
        "Ligand...5",
        "Protein...6",
        "Ligand...7",
        "Protein...8",
        "Ligand...9",
        "Protein...10",
        "Ligand...11",
        "Protein...12",
        "Ligand...13",
        "Protein...14",
        "Ligand...15",
        "Protein...16",
        "Ligand...17",
        "Protein...18",
        "Ligand...19",
        "Protein...20",
        "Ligand...21",
        "Protein...22",
        "Ligand...23",
        "Protein...24",
        "Ligand...25"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "analyze_norm",
      "title": "Analyze to Normalize",
      "topics": [
        "analyze_norm"
      ]
    },
    {
      "page": "condition_IDs",
      "title": "TSAR Condition IDs",
      "concept": [
        "TSA Summary Functions"
      ],
      "topics": [
        "condition_IDs"
      ]
    },
    {
      "page": "example_normalized_data",
      "title": "Example normalized TSA dataset",
      "topics": [
        "example_normalized_data"
      ]
    },
    {
      "page": "example_tsar_data",
      "title": "Example tsar_data file",
      "topics": [
        "example_tsar_data"
      ]
    },
    {
      "page": "gam_analysis",
      "title": "Analysis of all 96 wells through gam modeling",
      "concept": [
        "tsa_analysis"
      ],
      "topics": [
        "gam_analysis"
      ]
    },
    {
      "page": "get_legend",
      "title": "Extract ggplot2 legend",
      "concept": [
        "TSA Plots"
      ],
      "topics": [
        "get_legend"
      ]
    },
    {
      "page": "graph_tsar",
      "title": "Graph tsar_data",
      "concept": [
        "TSA Plots"
      ],
      "topics": [
        "graph_tsar"
      ]
    },
    {
      "page": "join_well_info",
      "title": "Well information input function",
      "concept": [
        "read_write_analysis"
      ],
      "topics": [
        "join_well_info"
      ]
    },
    {
      "page": "merge_norm",
      "title": "Merge and format norm_data into tsar_data",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "merge_norm"
      ]
    },
    {
      "page": "merge_tsa",
      "title": "Merge TSA Raw Data and Analysis Files",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "merge_TSA"
      ]
    },
    {
      "page": "model_beta",
      "title": "Beta-knot natural cubic spline model (Tm-centered via numerical_Tm)",
      "topics": [
        "model_beta"
      ]
    },
    {
      "page": "model_boltzmann",
      "title": "Boltzmann Modeling on TSA data",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "model_boltzmann"
      ]
    },
    {
      "page": "model_fit",
      "title": "Refit and calculate derivative function",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "model_fit"
      ]
    },
    {
      "page": "model_gam",
      "title": "Generalized Addidtive Modeling on TSA data",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "model_gam"
      ]
    },
    {
      "page": "normalize",
      "title": "Normalize Fluorescence",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "normalize"
      ]
    },
    {
      "page": "normalize_fluorescence",
      "title": "Normalize Fluorescence Curve",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "normalize_fluorescence"
      ]
    },
    {
      "page": "numerical_Tm",
      "title": "Numerical Tm by treating Tm as inflection point",
      "topics": [
        "numerical_Tm"
      ]
    },
    {
      "page": "qPCR_data1",
      "title": "qPCR_data1 Dataset",
      "topics": [
        "qPCR_data1"
      ]
    },
    {
      "page": "qPCR_data2",
      "title": "qPCR_data2 Dataset",
      "topics": [
        "qPCR_data2"
      ]
    },
    {
      "page": "read_analysis",
      "title": "Read TSA Analysis Data",
      "concept": [
        "Read TSA Data"
      ],
      "topics": [
        "read_analysis"
      ]
    },
    {
      "page": "read_raw_data",
      "title": "Read TSA Raw Data",
      "concept": [
        "Read TSA Data"
      ],
      "topics": [
        "read_raw_data"
      ]
    },
    {
      "page": "read_tsar",
      "title": "Read analysis result",
      "concept": [
        "read_write_analysis"
      ],
      "topics": [
        "read_tsar"
      ]
    },
    {
      "page": "remove_raw",
      "title": "Remove selected raw curves",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "remove_raw"
      ]
    },
    {
      "page": "rescale",
      "title": "Rescale values between minimum and maximum.",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "rescale"
      ]
    },
    {
      "page": "run_boltzmann",
      "title": "Run Boltzmann Modeling",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "run_boltzmann"
      ]
    },
    {
      "page": "screen",
      "title": "Screen raw curves",
      "concept": [
        "data_preprocess"
      ],
      "topics": [
        "screen"
      ]
    },
    {
      "page": "Tm_difference",
      "title": "Calculate Tm difference for all conditions",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "Tm_difference"
      ]
    },
    {
      "page": "Tm_est",
      "title": "Find inflection point function",
      "concept": [
        "tsa_analysis"
      ],
      "topics": [
        "Tm_est"
      ]
    },
    {
      "page": "tsa_average",
      "title": "Average TSA Curves",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "TSA_average"
      ]
    },
    {
      "page": "TSA_boxplot",
      "title": "TSA Box Plot",
      "concept": [
        "TSA Plots"
      ],
      "topics": [
        "TSA_boxplot"
      ]
    },
    {
      "page": "tsa_compare_plot",
      "title": "Compare TSA curves to control",
      "concept": [
        "TSA Plots"
      ],
      "topics": [
        "TSA_compare_plot"
      ]
    },
    {
      "page": "TSA_ligands",
      "title": "TSA Ligands",
      "concept": [
        "TSA Summary Functions"
      ],
      "topics": [
        "TSA_ligands"
      ]
    },
    {
      "page": "TSA_proteins",
      "title": "TSA Proteins",
      "concept": [
        "TSA Summary Functions"
      ],
      "topics": [
        "TSA_proteins"
      ]
    },
    {
      "page": "TSA_smoother_diagnostics",
      "title": "Diagnose Smoother Accuracy Across Conditions",
      "concept": [
        "Diagnostics"
      ],
      "topics": [
        "TSA_smoother_diagnostics"
      ]
    },
    {
      "page": "TSA_Tms",
      "title": "Reformat TSA data into TSA Tms",
      "concept": [
        "TSAR Formatting"
      ],
      "topics": [
        "TSA_Tms"
      ]
    },
    {
      "page": "TSA_wells_plot",
      "title": "TSA Well Curves Plot",
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