{
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  "Title": "RcisTarget Identify transcription factor binding motifs enriched\non a list of genes or genomic regions",
  "Version": "1.32.0",
  "Date": "2024-03-02",
  "Author": "Sara Aibar, Gert Hulselmans, Stein Aerts. Laboratory of\nComputational Biology. VIB-KU Leuven Center for Brain & Disease\nResearch. Leuven, Belgium",
  "Maintainer": "Gert Hulselmans <Gert.Hulselmans@kuleuven.be>",
  "Description": "RcisTarget identifies transcription factor binding motifs\n(TFBS) over-represented on a gene list. In a first step,\nRcisTarget selects DNA motifs that are significantly\nover-represented in the surroundings of the transcription start\nsite (TSS) of the genes in the gene-set. This is achieved by\nusing a database that contains genome-wide cross-species\nrankings for each motif. The motifs that are then annotated to\nTFs and those that have a high Normalized Enrichment Score\n(NES) are retained. Finally, for each motif and gene-set,\nRcisTarget predicts the candidate target genes (i.e. genes in\nthe gene-set that are ranked above the leading edge).",
  "URL": "http://scenic.aertslab.org",
  "License": "GPL-3",
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  "Date/Publication": "2026-04-28 12:47:10 UTC",
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      "headings": [
        "1. Prepare/download the input regions",
        "2. Load the RcisTarget databases",
        "3. Run the analysis"
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      "created": "2021-03-24 11:04:42",
      "modified": "2024-03-04 10:41:33",
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        "2. Create the background-ranking",
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      ],
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      "filename": "RcisTarget_MainTutorial.html",
      "title": "RcisTarget: Transcription factor binding motif enrichment",
      "engine": "knitr::rmarkdown",
      "headings": [
        "What is RcisTarget?",
        "Overview of the workflow",
        "Before starting",
        "Setup",
        "Some tips...",
        "Help",
        "Reports",
        "Running RcisTarget",
        "Input: Gene sets",
        "Required databases",
        "Gene-motif rankings",
        "Motif annotations",
        "Database example (subset)",
        "Running the analysis",
        "Advanced: Execute step by step",
        "1. Calculate enrichment",
        "2. Select significant motifs and/or annotate to TFs",
        "3. Identify the genes with the best enrichment for each Motif",
        "Output",
        "Follow up examples",
        "TFs annotated to the enriched motifs",
        "Building a network",
        "sessionInfo()"
      ],
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      "modified": "2022-10-31 12:14:00",
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