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  "Title": "Oscope - A statistical pipeline for identifying oscillatory\ngenes in unsynchronized single cell RNA-seq",
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  "Date": "2015-7-28",
  "Author": "Ning Leng",
  "Maintainer": "Ning Leng <lengning1@gmail.com>",
  "Description": "Oscope is a statistical pipeline developed to identifying\nand recovering the base cycle profiles of oscillating genes in\nan unsynchronized single cell RNA-seq experiment. The Oscope\npipeline includes three modules: a sine model module to search\nfor candidate oscillator pairs; a K-medoids clustering module\nto cluster candidate oscillators into groups; and an extended\nnearest insertion module to recover the base cycle order for\neach oscillator group.",
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      "title": "Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq",
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        "Oscope"
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      ]
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      "page": "OscopeENI",
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      ]
    },
    {
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      "topics": [
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