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 (3.21)

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] (ORCID: ), Wancen Mu [aut] (ORCID: ), Eric Davis [aut] (ORCID: ), Douglas Phanstiel [aut] (ORCID: ), Stuart Lee [aut] (ORCID: ), 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 "4.5") 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

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

browseVignettes("nullranges")

0. Introduction to nullranges	HTML	R Script
1. Introduction to bootRanges	HTML	R Script
2. Introduction to matchRanges	HTML	R Script
3. Matching case study I: CTCF occupancy	HTML	R Script
4. Matching case study II: CTCF orientation	HTML	R Script
5. Creating a pool set for matchRanges	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 years)
License	GPL-3
Depends
Imports	stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges
System Requirements
URL	https://nullranges.github.io/nullranges https://github.com/nullranges/nullranges
Bug Reports	https://support.bioconductor.org/tag/nullranges/

Suggests	testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, purrr, magrittr, tidyr, cobalt, DiagrammeR, tidySummarizedExperiment
Linking To
Enhances
Depends On Me
Imports Me	tidyomics
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	nullranges_1.13.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/nullranges/
Package Short Url	https://bioconductor.org/packages/nullranges/
Package Downloads Report	Download Stats