Bioconductor-mirror/NADfinder: Call wide peaks for sequencing data

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.

Getting started

Package details

AuthorJianhong Ou, Jun Yu, Paul Kaufman, Lihua Julie Zhu
Bioconductor views DNASeq GeneRegulation PeakDetection Sequencing
MaintainerJianhong Ou <[email protected]>, Lihua Julie Zhu <[email protected]>
LicenseGPL (>= 2)
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor-mirror/NADfinder documentation built on July 28, 2017, 4:27 a.m.