nullranges

This is the released version of nullranges; for the devel version, see nullranges.

Generation of null ranges via bootstrapping or covariate matching

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.nullranges

Bioconductor version: Release (3.22)

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 iD ORCID: 0000-0001-8401-0545 , Wancen Mu [aut] ORCID iD ORCID: 0000-0002-5061-7581 , Eric Davis [aut] ORCID iD ORCID: 0000-0003-4051-3217 , Douglas Phanstiel [aut] ORCID iD ORCID: 0000-0003-2123-0051 , Stuart Lee [aut] ORCID iD ORCID: 0000-0003-1179-8436 , 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")
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 1.16.0

In Bioconductor since BioC 3.14 (R-4.1) (4 years)

License GPL-3

Depends R (>= 4.2.0)

Imports stats, IRanges, GenomicRanges, Seqinfo, 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/

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me tidyomics

Links To Me

Build Report Build Report

Package Archives

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

Source Package nullranges_1.16.0.tar.gz

Windows Binary (x86_64) nullranges_1.15.1.zip

macOS Binary (x86_64) nullranges_1.16.0.tgz

macOS Binary (arm64) nullranges_1.16.0.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