Modular package for generation of sets of genomic features representing the null hypothesis. These can take the form of block bootstrap samples of ranges using the framework of Bickel et al 2010, or sets of control ranges that are matched across one or more covariates with a focal set. nullranges is designed to be inter-operable with other packages for analysis of genomic overlap enrichment, including the plyranges Bioconductor package.

An overview vignette can be found at the Get started tab above, while detailed vignettes on matching or bootstrapping can be found under Articles. The Reference tab lists function help pages.

This package can be installed via Bioconductor:

BiocManager::install("nullranges")

matchRanges manuscript:

Eric S. Davis, Wancen Mu, Stuart Lee, Mikhail G. Dozmorov, Michael I. Love, Douglas H. Phanstiel. (2022) "matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling." bioRxiv doi: 10.1101/2022.08.05.502985

bootRanges manuscript:

Wancen Mu, Eric S. Davis, Stuart Lee, Mikhail G. Dozmorov, Douglas H. Phanstiel, Michael I. Love. (2022) "bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing." bioRxiv doi: 10.1101/2022.09.02.506382

Additional tutorial material for performing tidy ranges analysis is currently being developed.

This work was funded by the Chan Zuckerberg Initiative as part of the EOSS grants.