Package: NADfinder 1.31.0

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'))

Peer review:

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.

sequencingdnaseqgeneregulationpeakdetection

4.00 score 1 scripts 218 downloads 17 exports 235 dependencies

Last updated 23 days agofrom:2b498e9ab5. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 31 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:backgroundCorrectionbutterFiltercallPeakscumulativePercentageexportSignalsgetCorrelationsgroupZscoresIntersectionNotStrictlog2sepeakdetplotSigsmoothRatiosByChromosometileCounttileCount2transformDatatrimPeakszscoreOverBck

Dependencies:abindade4annotateAnnotationDbiAnnotationFilterAnnotationHubaskpassATACseqQCbackportsbase64encbaselineBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcaToolscheckmateChIPpeakAnnoclicliprclusterCNErcodetoolscolorspacecorrplotcpp11crayoncsawcurldata.tableDBIdbplyrDelayedArraydeldirDEoptimRdichromatdigestDirichletMultinomialdplyredgeREmpiricalBrownsMethodensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGenomicScoresggplot2glueGO.dbgraphgridExtragrImportgtablegtoolsGvizHDF5ArrayhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2InteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclelimmalimSolvelocfitlpSolvemagrittrMASSmathjaxrMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemetapmetapodmgcvmimemnormtmotifStackmultcompmulttestmunsellmutossmvtnormnlmennetnumDerivopensslpillarpixmappkgconfigplogrplotrixplyrpngpolynompoweRlawpracmapreseqRprettyunitsprogressProtGenericspurrrpwalignqqconfquadprogquantregR.methodsS3R.ooR.utilsR6randomForestrappdirsRBGLrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppThreadRCurlRdpackreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrobustbaserpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssandwichsassscalesseqLogosignalsnsnowspSparseArraySparseMstatmodstrawrstringistringrSummarizedExperimentsurvivalsysTFBSToolsTFisherTFMPvalueTH.datatibbletidyrtidyselecttinytextrackViewertxdbmakertzdbUCSC.utilsuniversalmotifutf8VariantAnnotationvctrsVennDiagramviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioczoo

NADfinder Guide

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

Rendered fromNADfinder.Rmdusingknitr::rmarkdownon Oct 30 2024.

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