Package: NADfinder
Type: Package
Title: Call wide peaks for sequencing data
Version: 1.35.0
Encoding: UTF-8
Author: Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman,
        Lihua Julie Zhu
Maintainer: Jianhong Ou <jou@morgridge.org>, Lihua Julie Zhu
 <julie.zhu@umassmed.edu>
Description: Nucleolus is an important structure inside the nucleus in
        eukaryotic cells. It is the site for transcribing rDNA into
        rRNA and for assembling ribosomes, aka ribosome biogenesis. In
        addition, nucleoli are dynamic hubs through which numerous
        proteins shuttle and contact specific non-rDNA genomic loci.
        Deep sequencing analyses of DNA associated with isolated
        nucleoli (NAD- seq) have shown that specific loci, termed
        nucleolus- associated domains (NADs) form frequent three-
        dimensional associations with nucleoli. NAD-seq has been used
        to study the biological functions of NAD and the dynamics of
        NAD distribution during embryonic stem cell (ESC)
        differentiation. Here, we developed a Bioconductor package
        NADfinder for bioinformatic analysis of the NAD-seq data,
        including baseline correction, smoothing, normalization, peak
        calling, and annotation.
License: GPL (>= 2)
Depends: R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, S4Vectors,
        SummarizedExperiment
Imports: graphics, methods, baseline, signal, GenomicAlignments,
        GenomeInfoDb, rtracklayer, limma, trackViewer, stats, utils,
        Rsamtools, metap, EmpiricalBrownsMethod,ATACseqQC, corrplot,
        csaw
Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10,
        testthat, BiocManager, rmarkdown
biocViews: Sequencing, DNASeq, GeneRegulation, PeakDetection
LazyData: TRUE
VignetteBuilder: knitr
RoxygenNote: 7.1.1
Config/pak/sysreqs: libfftw3-dev make libgsl0-dev libbz2-dev libicu-dev
        libjpeg-dev liblzma-dev libpng-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:37:48 UTC
RemoteUrl: https://github.com/bioc/NADfinder
RemoteRef: HEAD
RemoteSha: 7e7a8873d12189519a3b18cf7c7e2d037d2d4c2d
NeedsCompilation: no
Packaged: 2026-02-08 10:06:52 UTC; root
Built: R 4.6.0; ; 2026-02-08 10:32:39 UTC; unix
