Package: NADfinder Type: Package Title: Call wide peaks for sequencing data Version: 1.37.0 Encoding: UTF-8 Author: Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman, Lihua Julie Zhu Maintainer: Jianhong Ou , Lihua Julie Zhu 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: cmake libfftw3-dev make libgsl0-dev libbz2-dev libicu-dev libjpeg-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:45:24 UTC RemoteUrl: https://github.com/bioc/NADfinder RemoteRef: HEAD RemoteSha: b87312bce6fee4a3580cf81398439d5087fd565e NeedsCompilation: no Packaged: 2026-07-04 05:38:15 UTC; root