nullranges

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see nullranges.

Generation of null ranges via bootstrapping or covariate matching

Bioconductor version: 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 (!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. 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 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 1.2.0

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, ks, speedglm, data.table, progress, ggridges

System Requirements

URL https://nullranges.github.io/nullranges

Bug Reports https://support.bioconductor.org/t/nullranges/

Suggests testthat, knitr, rmarkdown, DNAcopy, RcppHMM, AnnotationHub, nullrangesData, excluderanges, ensembldb, EnsDb.Hsapiens.v86, microbenchmark, patchwork, plotgardener, magrittr, tidyr, cobalt

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