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  "_id": "6a49434818cdde069385eab9",
  "Package": "FindIT2",
  "Title": "find influential TF and Target based on multi-omics data",
  "Version": "1.19.0",
  "Authors@R": "c(\nperson(\"Guandong\", \"Shang\", role = c(\"aut\", \"cre\"),\nemail = \"shangguandong1996@163.com\",\ncomment = c(ORCID = \"0000-0002-9509-0314\"))\n)",
  "Description": "This package implements functions to find influential TF\nand target based on different input type. It have five module:\nMulti-peak multi-gene annotaion(mmPeakAnno module), Calculate\nregulation potential(calcRP module), Find influential Target\nbased on ChIP-Seq and RNA-Seq data(Find influential Target\nmodule), Find influential TF based on different input(Find\ninfluential TF module), Calculate peak-gene or peak-peak\ncorrelation(peakGeneCor module). And there are also some other\nuseful function like integrate different source information,\ncalculate jaccard similarity for your TF.",
  "License": "Artistic-2.0",
  "URL": "https://github.com/shangguandong1996/FindIT2",
  "BugReports": "https://support.bioconductor.org/t/FindIT2",
  "biocViews": "Software, Annotation, ChIPSeq, ATACSeq, GeneRegulation,\nMultipleComparison, GeneTarget",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:26 UTC",
  "RemoteUrl": "https://github.com/bioc/FindIT2",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-04 12:18:32 UTC",
    "User": "root"
  },
  "Author": "Guandong Shang [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-9509-0314>)",
  "Maintainer": "Guandong Shang <shangguandong1996@163.com>",
  "_user": "bioc",
  "_type": "src",
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  "_expires": "2026-10-12T17:30:46.000Z",
  "_created": "2026-07-04T12:18:32.000Z",
  "_published": "2026-07-04T17:30:48.331Z",
  "_bioccheck": {
    "error": 0,
    "warning": 0,
    "note": 12
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  "_host": "GitHub-Actions",
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  "_upstream": "https://github.com/bioc/FindIT2",
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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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  "_maintainer": {
    "name": "Guandong Shang",
    "email": "shangguandong1996@163.com",
    "login": "shangguandong1996",
    "description": "Postgraduate, interested in Epigenomics and Bioinformatics",
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    "findIT_enrichFisher",
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    "peakGeneCor",
    "plot_annoDistance",
    "plot_peakGeneAlias_summary",
    "plot_peakGeneCor"
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      "page": "ATAC_normCount",
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