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nullranges

Generation of null ranges via bootstrapping or covariate matching

Bioconductor version: 3.23 · Package version: 1.18.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("nullranges")

Details

MaintainerMichael Love <michaelisaiahlove@gmail.com>
AuthorMichael Love [aut, cre] (ORCID: <https://orcid.org/0000-0001-8401-0545>), Wancen Mu [aut] (ORCID: <https://orcid.org/0000-0002-5061-7581>), Eric Davis [aut] (ORCID: <https://orcid.org/0000-0003-4051-3217>), Douglas Phanstiel [aut] (ORCID: <https://orcid.org/0000-0003-2123-0051>), Stuart Lee [aut] (ORCID: <https://orcid.org/0000-0003-1179-8436>), Mikhail Dozmorov [ctb], Tim Triche [ctb], CZI [fnd]
LicenseGPL-3
URLhttps://nullranges.github.io/nullranges, https://github.com/nullranges/nullranges
Bug Reportshttps://support.bioconductor.org/tag/nullranges/
Downloads rank401
Source branchRELEASE_3_23
biocViewsATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization

Documentation

Download

Dependencies

Depends: R (>= 4.2.0)

Imports: stats, IRanges, GenomicRanges, Seqinfo, methods, rlang, S4Vectors, scales, InteractionSet, ggplot2, grDevices, plyranges, data.table, progress, ggridges

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

Reverse dependencies

Suggests Me (1): tidyomics