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An R package that provides functions for 1) calculating and 2) visualizing a variety of statistics for a collection of genomic ranges. If you have a set of genomic ranges, such as a BED file the GenomicDistributions R package can help you to explore, annotate, visualize,and compare it.
Installing
Main package
With Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicDistributions")Or from GitHub:
devtools::install_github("databio/GenomicDistributions")Data package
GenomicDistributionsData: includes full data files, too large to include in GenomicDistributions
Quick start
See the vignettes for more information: http://code.databio.org/GenomicDistributions
Building long vignettes
In the long_vignettes are vignettes that require large external data and take a long time to run. Therefore, they should be pre-built. You can render them manually by running long_vignettes/render-long-vignettes.R. This will use knitr to run the vignette and put the result into the vignettes folder, along with output figures.
Cite GenomicDistributions:
Kupkova K., Mosquera J.V., Smith J.P., Stolarczyk M, Danehy T., Lawson J.T., Rogers S., LeRoy N., Sheffield N.C. GenomicDistributions: fast analysis of genomic intervals with Bioconductor. BMC Genomics 23, 299 (2022). https://doi.org/10.1186/s12864-022-08467-y