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  "Title": "TCC: Differential expression analysis for tag count data with\nrobust normalization strategies",
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  "Author": "Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji\nKadota",
  "Maintainer": "Jianqiang Sun <sun@bitdessin.dev>, Tomoaki Nishiyama\n<tomoakin@staff.kanazawa-u.ac.jp>",
  "Description": "This package provides a series of functions for performing\ndifferential expression analysis from RNA-seq count data using\nrobust normalization strategy (called DEGES). The basic idea of\nDEGES is that potential differentially expressed genes or\ntranscripts (DEGs) among compared samples should be removed\nbefore data normalization to obtain a well-ranked gene list\nwhere true DEGs are top-ranked and non-DEGs are bottom ranked.\nThis can be done by performing a multi-step normalization\nstrategy (called DEGES for DEG elimination strategy). A major\ncharacteristic of TCC is to provide the robust normalization\nmethods for several kinds of count data (two-group with or\nwithout replicates, multi-group/multi-factor, and so on) by\nvirtue of the use of combinations of functions in depended\npackages.",
  "License": "GPL-2",
  "Copyright": "Authors listed above",
  "biocViews": "ImmunoOncology, Sequencing, DifferentialExpression, RNASeq",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-08-11 12:29:39 UTC",
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      ],
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      "tojson": true
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        "array"
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        "tissue4",
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        "tissue9",
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      "tojson": true
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      "title": "DNA microarray data set",
      "object": "nakai",
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      "class": [
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        "array"
      ],
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        "Liver_fed",
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      "page": "arab",
      "title": "Arabidopsis RNA-Seq data set",
      "topics": [
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      ]
    },
    {
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      "title": "Calculate AUC value from a TCC-class object",
      "topics": [
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      ]
    },
    {
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      "title": "Calculate normalization factors",
      "topics": [
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        "calcNormFactors,DGEList-method",
        "calcNormFactors,TCC-method"
      ]
    },
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      "topics": [
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      ]
    },
    {
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      "topics": [
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      ]
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    {
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      "topics": [
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      ]
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      "topics": [
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      ]
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      "topics": [
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      "topics": [
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    },
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      "title": "DNA microarray data set",
      "topics": [
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        "plot.TCC"
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      "topics": [
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      "topics": [
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        "TCC"
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