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GenomicDistributions

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Bioconductor version: 3.23 · Package version: 1.20.0

If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.

Installation

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

BiocManager::install("GenomicDistributions")

Details

MaintainerKristyna Kupkova <kristynakupkova@gmail.com>
AuthorKristyna Kupkova [aut, cre], Jose Verdezoto [aut], Tessa Danehy [aut], John Lawson [aut], Jose Verdezoto [aut], Michal Stolarczyk [aut], Jason Smith [aut], Bingjie Xue [aut], Sophia Rogers [aut], John Stubbs [aut], Nathan C. Sheffield [aut]
LicenseBSD_2_clause + file LICENSE
URLhttp://code.databio.org/GenomicDistributions
Bug Reportshttp://github.com/databio/GenomicDistributions
Downloads rank527
Source branchRELEASE_3_23
biocViewsCoverage, DataRepresentation, FunctionalGenomics, GenomeAnnotation, GenomeAssembly, Sequencing, Software, Visualization

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageGenomicDistributions_1.20.0.tar.gz
Windows binary (x86_64)GenomicDistributions_1.20.0.zip
macOS binary (arm64)GenomicDistributions_1.20.0.tgz
macOS binary (x86_64)GenomicDistributions_1.20.0.tgz
Dependencies

Depends: R (>= 4.0), IRanges, GenomicRanges

Imports: data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats

Suggests: AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData

Enhances: BSgenome, extrafont, ensembldb, GenomicFeatures