nullranges

DOI: 10.18129/B9.bioc.nullranges  

Generation of null ranges via bootstrapping or covariate matching

Bioconductor version: Release (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 gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("nullranges")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("nullranges")

 

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

Details

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
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
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	nullranges_1.4.0.tar.gz
Windows Binary	nullranges_1.4.0.zip (64-bit only)
macOS Binary (x86_64)	nullranges_1.4.0.tgz
macOS Binary (arm64)	nullranges_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nullranges
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nullranges
Bioc Package Browser	https://code.bioconductor.org/browse/nullranges/
Package Short Url	https://bioconductor.org/packages/nullranges/
Package Downloads Report	Download Stats