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DOI: 10.18129/B9.bioc.NADfinder    

Call wide peaks for sequencing data

Bioconductor version: Release (3.5)

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 nucleolar- 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 normalization, smoothing, peak calling, peak trimming and annotation.

Author: Jianhong Ou, Jun Yu, Anastassiia Vertii, Paul Kaufman, Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at>, Lihua Julie Zhu <julie.zhu at>

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biocViews DNASeq, GeneRegulation, PeakDetection, Sequencing, Software
Version 1.0.1
In Bioconductor since BioC 3.5 (R-3.4) (0.5 years)
License GPL (>= 2)
Depends R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors
Imports graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, SummarizedExperiment, limma, trackViewer, stats, utils
Suggests RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat
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