Package: NADfinder 1.29.0

Jianhong Ou

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 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.

Authors:Jianhong Ou, Haibo Liu, Jun Yu, Hervé Pagès, Paul Kaufman, Lihua Julie Zhu

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NADfinder.pdf |NADfinder.html✨
NADfinder/json (API)
NEWS

# Install 'NADfinder' in R:

install.packages('NADfinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

single.count - Counts data for chromosome 18 for an experiment of a single pair of samples
triplicate.count - Counts data for chromosome 18 for an expriment with triplicates

On BioConductor:NADfinder-1.29.0(bioc 3.20)NADfinder-1.28.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

17 exports 1.00 score 236 dependencies

Last updated 2 months agofrom:e8ed28e16e

Exports:backgroundCorrection butterFilter callPeaks cumulativePercentage exportSignals getCorrelations groupZscores IntersectionNotStrict log2se peakdet plotSig smoothRatiosByChromosome tileCount tileCount2 transformData trimPeaks zscoreOverBck

Dependencies:abind ade4 annotate AnnotationDbi AnnotationFilter AnnotationHub askpass ATACseqQC backports base64enc baseline BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem caTools checkmate ChIPpeakAnno cli clipr cluster CNEr codetools colorspace corrplot cpp11 crayon csaw curl data.table DBI dbplyr DelayedArray deldir DEoptimR dichromat digest DirichletMultinomial dplyr edgeR EmpiricalBrownsMethod ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GenomicScores ggplot2 glue GO.db graph gridExtra grImport gtable gtools Gviz HDF5Array highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph InteractionSet interp IRanges isoband jpeg jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma limSolve locfit lpSolve magrittr MASS mathjaxr Matrix MatrixGenerics MatrixModels matrixStats memoise metap metapod mgcv mime mnormt motifStack multcomp multtest munsell mutoss mvtnorm nlme nnet numDeriv openssl pillar pixmap pkgconfig plogr plotrix plyr png polynom poweRlaw pracma preseqR prettyunits progress ProtGenerics purrr pwalign qqconf quadprog quantreg R.methodsS3 R.oo R.utils R6 randomForest rappdirs RBGL rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppThread RCurl Rdpack readr regioneR reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown robustbase rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sandwich sass scales seqLogo signal sn snow sp SparseArray SparseM statmod strawr stringi stringr SummarizedExperiment survival sys TFBSTools TFisher TFMPvalue TH.data tibble tidyr tidyselect tinytex trackViewer txdbmaker tzdb UCSC.utils universalmotif utf8 VariantAnnotation vctrs VennDiagram viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

NADfinder Guide

Jianhong Ou, Haibo Liu, Jun Yu, Paul Kaufman and Lihua Julie Zhu

Rendered fromNADfinder.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2019-08-15
Started: 2017-03-31

Help page	Topics
Identify nucleolus-associated domains (NADs) from NAD-seq	NADfinder-package NADfinder
Correct ratios for background	backgroundCorrection
Low pass filter on ratios by butterworth filter	butterFilter
Call peaks using transformed, background corrected, and smoothed ratios with biological replicates	callPeaks
Perform overlap queries between reads and genome by sliding windows Count reads over sliding windows.	computeLibSizeChrom
Plot the cumulative percentage of tag allocation	cumulativePercentage
Output signals for visualization	exportSignals
Get correlation coefficinets and p-values between biological replicates	getCorrelations
Calculate z-scores for each peak	groupZscores
Count reads overlapping genomic ranges	IntersectionNotStrict
calculate the log2 transformed ratios for SummarizedExperiment class	log2se
Detect peak positions	peakdet
Plot signals with ideograms	plotSig
Counts data for chromosome 18 for an experiment of a single pair of samples	single.count
Backgound correction and signal smoothing per chromosome	smoothRatiosByChromosome
Perform overlap queries between reads and genome by windows	tileCount
Perform overlap queries between reads and genome by sliding windows Count reads over sliding windows.	tileCount2
transform counts to log2 cpm ratios, log2 ratios or log2 odds ratios	transformData
Trim peaks	trimPeaks
Counts data for chromosome 18 for an expriment with triplicates	triplicate.count
Z-scores over the background	zscoreOverBck

Package: NADfinder 1.29.0

NADfinder: Call wide peaks for sequencing data

NADfinder Guide

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