DOI: 10.18129/B9.bioc.nullranges  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see nullranges.

Generation of null ranges via bootstrapping or covariate matching

Bioconductor version: 3.16

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrap samples of ranges (using the block bootstrap framework of Bickel et al 2010), or sets of control ranges that are matched across one or more covariates. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.

Author: Michael Love [aut, cre] , Wancen Mu [aut] , Eric Davis [aut] , Douglas Phanstiel [aut] , Stuart Lee [aut] , Mikhail Dozmorov [ctb], Tim Triche [ctb], CZI [fnd]

Maintainer: Michael Love <michaelisaiahlove at>

Citation (from within R, enter citation("nullranges")):


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HTML R Script 0. Introduction to nullranges
HTML R Script 1. Overview of matchRanges
HTML R Script 2. Case study I: CTCF occupancy
HTML R Script 3. Case study II: CTCF orientation
HTML R Script 4. Segmented block bootstrap
HTML R Script 5. Unsegmented block bootstrap
PDF   Reference Manual
Text   NEWS


biocViews ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL-3
Imports stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, ks, speedglm, data.table, progress, ggridges
Suggests testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener, magrittr, tidyr, cobalt
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