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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
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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 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 |
| Reference Manual |
Details
| 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 |
| 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_1.0.1.tar.gz |
| Windows Binary | NADfinder_1.0.1.zip |
| Mac OS X 10.11 (El Capitan) | NADfinder_1.0.1.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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