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nullranges

Generation of null ranges via bootstrapping or covariate matching


Bioconductor version: Release (3.18)

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 "4.3") 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")
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

Details

biocViews ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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/
See More
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
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Package Archives

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

Source Package nullranges_1.8.0.tar.gz
Windows Binary nullranges_1.8.0.zip
macOS Binary (x86_64) nullranges_1.8.0.tgz
macOS Binary (arm64) nullranges_1.8.0.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