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  "Title": "A Curated ChIP-Seq Dataset of MDI-induced Differentiated\nAdipocytes (3T3-L1)",
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  "Description": "A curated dataset of publicly available ChIP-sequencing of\ntranscription factors, chromatin remodelers and histone\nmodifications in the 3T3-L1 pre-adipocyte cell line. The\npackage document the data collection, pre-processing and\nprocessing of the data. In addition to the documentation, the\npackage contains the scripts that was used to generated the\ndata.",
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      "title": "Using curatedAdipoChIP",
      "author": "Mahmoud Ahmed",
      "engine": "knitr::rmarkdown",
      "headings": [
        "curatedAdipoChIP",
        "Overview",
        "Introduction",
        "What is curatedAdipoChIP?",
        "What is contained in curatedAdipoChIP?",
        "What is curatedAdipoChIP for?",
        "Installation",
        "Docker image",
        "Generating curatedAdipoChIP",
        "Search starategy & data collection",
        "Pre-processing",
        "1. Downloading data download_fastq",
        "2. Making a genome index make_index",
        "3. Dowinloading annotations get_annotation",
        "4. Aligning reads align_reads",
        "5. Calling peaks peak_calling",
        "6. Making a peakset get_peakset",
        "7. Counting reads in peaks count_features",
        "8. Quality assessment fastqc",
        "Processing",
        "Making a summarized experiment object peak_object",
        "Exploring the peak_counts object",
        "Summary of the studies in the dataset",
        "Example of using curatedAdipoChIP",
        "Motivation",
        "Subsetting the object to samples and peaks of interest",
        "Filtering low quality samples",
        "Filtering peaks with low counts",
        "Check sample reproducibility",
        "Applying differential binding using DESeq2",
        "Next!",
        "Citing the studies in this subset of the data",
        "Citing curatedAdipoChIP",
        "Session Info"
      ],
      "created": "2019-04-09 04:43:01",
      "modified": "2019-04-12 01:19:14",
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