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      "title": "filterChromosomes listChrTypes",
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      "title": "regioneR: Association analysis of genomic regions based on permutation tests",
      "author": "Bernat Gel (bgel@igtp.cat), Anna Diez-Villanueva (adiez@iconcologia.net) and Roberto Malinverni (rmalinverni@carrerasresearch.org)",
      "engine": "knitr::rmarkdown",
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        "Quick Start",
        "Permutation tests",
        "How does a permutation test work?",
        "How to perform a permutation test with r BiocStyle::Biocpkg(\"regioneR\")",
        "A note on the number of permutations",
        "Randomization Functions",
        "randomizeRegions",
        "circularRandomizeRegions",
        "resampleRegions",
        "Evaluation Functions",
        "numOverlaps",
        "meanDistance",
        "meanInRegion",
        "Custom Functions",
        "Custom Evaluation",
        "Custom Randomization",
        "A note on reproducibility",
        "Local Z-score",
        "Region Sets",
        "Genomes and Masks",
        "Genomes",
        "Masks",
        "How to retrieve a genome and mask",
        "Filtering Chromosomes",
        "Region Set Helper Functions",
        "Functions operating on a single RS",
        "Functions operating on two RS",
        "Other Functions: functions not returning a GRanges object",
        "Usage Examples",
        "Example 1: CpG Islands and Gene Promoters. A basic example.",
        "Question: Are Cpg islands and promoters associated?",
        "Brief Problem Description:",
        "Datasets:",
        "Step-by-step analysis:",
        "References:",
        "Example 2: Analysis of ChIP-seq peaks. Advanced usage and local Z-score.",
        "Question: In the cell line Hepg2 (Human hepatocellular carcinoma ), is Rad21 (Cohesin) associated with CTCF? And with gene promoters? Are these associations different?",
        "Benchmarks and Performance",
        "Technical Considerations",
        "Memoisation",
        "Session Info"
      ],
      "created": "2018-08-13 14:06:28",
      "modified": "2019-07-16 16:09:32",
      "commits": 4
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