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  "Title": "Call wide peaks for sequencing data",
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  "Encoding": "UTF-8",
  "Author": "Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman,\nLihua Julie Zhu",
  "Maintainer": "Jianhong Ou <jou@morgridge.org>, Lihua Julie Zhu\n<julie.zhu@umassmed.edu>",
  "Description": "Nucleolus is an important structure inside the nucleus in\neukaryotic cells. It is the site for transcribing rDNA into\nrRNA and for assembling ribosomes, aka ribosome biogenesis. In\naddition, nucleoli are dynamic hubs through which numerous\nproteins shuttle and contact specific non-rDNA genomic loci.\nDeep sequencing analyses of DNA associated with isolated\nnucleoli (NAD- seq) have shown that specific loci, termed\nnucleolus- associated domains (NADs) form frequent three-\ndimensional associations with nucleoli. NAD-seq has been used\nto study the biological functions of NAD and the dynamics of\nNAD distribution during embryonic stem cell (ESC)\ndifferentiation. Here, we developed a Bioconductor package\nNADfinder for bioinformatic analysis of the NAD-seq data,\nincluding baseline correction, smoothing, normalization, peak\ncalling, and annotation.",
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  "Date/Publication": "2026-04-28 12:45:24 UTC",
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    {
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      "engine": "knitr::rmarkdown",
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