nullranges
This is the development version of nullranges; for the stable release version, see nullranges.
Generation of null ranges via bootstrapping or covariate matching
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.19.0 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | nullranges_1.19.0.tar.gz |
| Windows Binary (x86_64) | nullranges_1.19.0.zip |
| macOS Binary (big-sur-x86_64) | nullranges_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | nullranges_1.19.0.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 |