NADfinder

Call wide peaks for sequencing data

Bioconductor version: Release (3.19)

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.

Author: Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman, Lihua Julie Zhu

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

Citation (from within R, enter citation("NADfinder")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("NADfinder")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("NADfinder")

NADfinder.html	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNASeq, GeneRegulation, PeakDetection, Sequencing, Software
Version	1.28.0
In Bioconductor since	BioC 3.5 (R-3.4) (7.5 years)
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
System Requirements
URL

Suggests	RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown
Linking To
Enhances
Depends On Me
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Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	NADfinder_1.28.0.tar.gz
Windows Binary (x86_64)	NADfinder_1.28.0.zip
macOS Binary (x86_64)	NADfinder_1.28.0.tgz
macOS Binary (arm64)	NADfinder_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NADfinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NADfinder
Bioc Package Browser	https://code.bioconductor.org/browse/NADfinder/
Package Short Url	https://bioconductor.org/packages/NADfinder/
Package Downloads Report	Download Stats