NADfinder
Call wide peaks for sequencing data
Bioconductor version: 3.23 · Package version: 1.36.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NADfinder")Details
| Maintainer | Jianhong Ou <jou@morgridge.org>, Lihua Julie Zhu <julie.zhu@umassmed.edu> |
| Author | Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman, Lihua Julie Zhu |
| License | GPL (>= 2) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNASeq, GeneRegulation, PeakDetection, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/NADfinder/ |
Citation
From within R, enter citation("NADfinder"):
Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman, Lihua Julie Zhu. NADfinder: Call wide peaks for sequencing data. doi:10.18129/B9.bioc.NADfinder, R package version 1.36.0, https://bioconductor.org/packages/NADfinder.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | NADfinder_1.36.0.tar.gz |
| Windows binary (x86_64) | NADfinder_1.36.0.zip |
| macOS binary (arm64) | NADfinder_1.36.0.tgz |
| macOS binary (x86_64) | NADfinder_1.36.0.tgz |
Dependencies
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
Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager, rmarkdown