nullranges
Generation of null ranges via bootstrapping or covariate matching
Bioconductor version: Release (3.17)
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")):
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 | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization |
| Version | 1.6.2 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2 years) |
| License | GPL-3 |
| Depends | |
| Imports | stats, IRanges, GenomicRanges, GenomeInfoDb, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges |
| Linking To | |
| 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 |
| System Requirements | |
| Enhances | |
| URL | https://nullranges.github.io/nullranges https://github.com/nullranges/nullranges |
| Bug Reports | https://support.bioconductor.org/tag/nullranges/ |
See More
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | nullranges_1.6.2.tar.gz |
| Windows Binary | nullranges_1.6.2.zip |
| macOS Binary (x86_64) | nullranges_1.6.2.tgz |
| macOS Binary (arm64) | nullranges_1.6.2.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 |
| Old Source Packages for BioC 3.17 | Source Archive |