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
| Maintainer | Michael Love <michaelisaiahlove@gmail.com> |
| Author | Michael 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] |
| License | GPL-3 |
| URL | https://nullranges.github.io/nullranges, https://github.com/nullranges/nullranges |
| Bug Reports | https://support.bioconductor.org/tag/nullranges/ |
| Downloads rank | 401 |
| Source branch | RELEASE_3_23 |
| biocViews | ATACSeq, Annotation, ChIPSeq, DNaseSeq, Epigenetics, FunctionalGenomics, GeneRegulation, GeneSetEnrichment, GeneTarget, GenomeAnnotation, GenomeWideAssociation, HiddenMarkovModel, HistoneModification, RNASeq, Software, Visualization |
Documentation
- Introduction to nullranges
- Introduction to bootRanges
- Introduction to matchRanges
- Matching case study I: CTCF occupancy
- Matching case study II: CTCF orientation
- Creating a pool set for matchRanges
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