NADfinder
Call wide peaks for sequencing data
Bioconductor version: Release (3.17)
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("NADfinder")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | DNASeq, GeneRegulation, PeakDetection, Sequencing, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (6.5 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 |
| Linking To | |
| Suggests | RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown |
| System Requirements | |
| Enhances | |
| URL |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NADfinder_1.24.0.tar.gz |
| Windows Binary | NADfinder_1.24.0.zip |
| macOS Binary (x86_64) | NADfinder_1.24.0.tgz |
| macOS Binary (arm64) | NADfinder_1.24.0.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 |