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 (3.15)

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>

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

Installation

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

if (!requireNamespace("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

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 1.1.1
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
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, nullrangesData, excluderanges, EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener, magrittr, cobalt
SystemRequirements
Enhances
URL https://nullranges.github.io/nullranges
BugReports https://support.bioconductor.org/t/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_1.1.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra) nullranges_1.1.1.tgz
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

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