{
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  "Package": "lionessR",
  "Title": "Modeling networks for individual samples using LIONESS",
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  "Description": "LIONESS, or Linear Interpolation to Obtain Network\nEstimates for Single Samples, can be used to reconstruct\nsingle-sample networks (https://arxiv.org/abs/1505.06440). This\ncode implements the LIONESS equation in the lioness function in\nR to reconstruct single-sample networks. The default network\nreconstruction method we use is based on Pearson correlation.\nHowever, lionessR can run on any network reconstruction\nalgorithms that returns a complete, weighted adjacency matrix.\nlionessR works for both unipartite and bipartite networks.",
  "Authors@R": "c(person(c(\"Marieke\", \"Lydia\"), \"Kuijjer\", \nrole = c(\"aut\"),\nemail = \"marieke.kuijjer@ncmm.uio.no\",\ncomment = c(ORCID = \"0000-0001-6280-3130\")),\nperson(\"Ping-Han\", \"Hsieh\",\nrole = c(\"cre\"),\nemail = \"dn070017@gmail.com\",\ncomment = c(ORCID = \"0000-0003-3054-1409\")))",
  "License": "MIT + file LICENSE",
  "LazyData": "TRUE",
  "biocViews": "Network, NetworkInference, GeneExpression",
  "BugReports": "https://github.com/mararie/lionessR/issues",
  "URL": "https://github.com/mararie/lionessR",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:50:59 UTC",
  "RemoteUrl": "https://github.com/bioc/lionessR",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
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    "User": "root"
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  "Author": "Marieke Lydia Kuijjer [aut] (ORCID:\n<https://orcid.org/0000-0001-6280-3130>),\nPing-Han Hsieh [cre] (ORCID: <https://orcid.org/0000-0003-3054-1409>)",
  "Maintainer": "Ping-Han Hsieh <dn070017@gmail.com>",
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    "warning": 1,
    "note": 8
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    "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",
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    "email": "dn070017@gmail.com",
    "login": "dn070017",
    "description": "I am a doctoral candidate, working at the Center for Molecular Medicine Norway and Department of Informatics, University of Oslo.\n",
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  "_contributors": [
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    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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  "_cranurl": false,
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      "created": "2018-08-17 21:17:48",
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