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# nullranges <img id="nullranges_logo" src="man/figures/logo.png" align="right" width="125"/> [![R build status](]( ## Generation of null ranges via bootstrapping or covariate matching 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, including a **decision tree** informing which type of methods may be most appropriate, whether *matching* or *bootstrapping*. Detailed vignettes on matching or bootstrapping can be found under `Articles`. The `Reference` tab lists function help pages. ## Installation This package can be installed via Bioconductor: ``` BiocManager::install("nullranges") ``` Installing nullranges and all of its dependencies on Mac or Windows with binaries will be very fast (a minute or so). For installing on Ubuntu, note that many *nullranges* packages are available as binaries, which greatly speeds up installation. Follow the instructions for [r2u](, then install the following via `apt`: ``` r-cran-tidyverse r-cran-ks r-cran-speedglm r-cran-data.table r-cran-progress r-cran-ggridges r-cran-biocmanager r-bioc-rtracklayer r-bioc-genomicalignments r-bioc-interactionset ``` ## Papers *matchRanges* paper: Eric S. Davis, Wancen Mu, Stuart Lee, Mikhail G. Dozmorov, Michael I. Love, Douglas H. Phanstiel. (2023) "matchRanges: Generating null hypothesis genomic ranges via covariate-matched sampling." *Bioinformatics* [doi: 10.1093/bioinformatics/btad197]( *bootRanges* paper: Wancen Mu, Eric S. Davis, Stuart Lee, Mikhail G. Dozmorov, Douglas H. Phanstiel, Michael I. Love. (2023) "bootRanges: Flexible generation of null sets of genomic ranges for hypothesis testing." *Bioinformatics* [doi: 10.1093/bioinformatics/btad190]( ## Tidy Ranges Tutorial Additional tutorial material for performing [tidy ranges]( analysis is currently being developed. ## Funding This work was funded by the Chan Zuckerberg Initiative as part of the EOSS grants. ![](man/figures/czi.png)