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
git_url: https://git.bioconductor.org/packages/NADfinder
git_branch: devel
git_last_commit: 7e7a887
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
Date/Publication: 2025-12-10
NeedsCompilation: no
Packaged: 2025-12-10 22:21:50 UTC; biocbuild
Built: R 4.6.0; ; 2025-12-11 05:09:59 UTC; unix
