To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("NADfinder")

In most cases, you don't need to download the package archive at all.

NADfinder

DOI: 10.18129/B9.bioc.NADfinder    

Call wide peaks for sequencing data

Bioconductor version: Release (3.6)

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, Paul Kaufman, Lihua Julie Zhu

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("NADfinder")

Documentation

HTML R Script NADfinder Vignette
PDF   Reference Manual

Details

biocViews DNASeq, GeneRegulation, PeakDetection, Sequencing, Software
Version 1.2.0
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
LinkingTo
Suggests RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package NADfinder_1.2.0.tar.gz
Windows Binary NADfinder_1.2.0.zip
Mac OS X 10.11 (El Capitan) NADfinder_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NADfinder
Package Short Url http://bioconductor.org/packages/NADfinder/
Package Downloads Report Download Stats

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