nullranges

DOI: 10.18129/B9.bioc.nullranges    

This is the development version of nullranges; for the stable release version, see nullranges.

Generation of null ranges via bootstrapping or covariate matching

Bioconductor version: Development (3.17)

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 gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("nullranges")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF		Reference Manual

Details

biocViews	ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization
Version	1.5.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	GPL-3
Depends
Imports	stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, ks, speedglm, data.table, progress, ggridges
LinkingTo
Suggests	testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener, magrittr, tidyr, cobalt
SystemRequirements
Enhances
URL	https://nullranges.github.io/nullranges https://github.com/nullranges/nullranges
BugReports	https://support.bioconductor.org/tag/nullranges/
Depends On Me
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/nullranges
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nullranges
Package Short Url	https://bioconductor.org/packages/nullranges/
Package Downloads Report	Download Stats