nullranges
This is the released version of nullranges; for the devel version, see nullranges.
Generation of null ranges via bootstrapping or covariate matching
Bioconductor version: Release (3.23)
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("nullranges")):Michael Love, Wancen Mu, Eric Davis, Douglas Phanstiel, Stuart Lee. nullranges: Generation of null ranges via bootstrapping or covariate matching. doi:10.18129/B9.bioc.nullranges, R package version 1.18.0, https://bioconductor.org/packages/nullranges.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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")| 1. Introduction to bootRanges | HTML | R Script |
| 4. Matching case study II: CTCF orientation | HTML | R Script |
| 3. Matching case study I: CTCF occupancy | HTML | R Script |
| 5. Creating a pool set for matchRanges | HTML | R Script |
| 2. Introduction to matchRanges | HTML | R Script |
| 0. Introduction to nullranges | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 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/ |
See More
| Suggests | testthat, knitr, rmarkdown, ks, DNAcopy, RcppHMM, AnnotationHub, ExperimentHub, GenomeInfoDb, nullrangesData, ensembldb, EnsDb.Hsapiens.v86, BSgenome.Hsapiens.UCSC.hg38, patchwork, plotgardener, dplyr, magrittr, tidyr, cobalt, DiagrammeR, MatchIt, mariner |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | tidyomics |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | nullranges_1.18.0.tar.gz |
| Windows Binary (x86_64) | nullranges_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | nullranges_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | nullranges_1.18.0.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 |