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GenomicDistributions

GenomicDistributions: fast analysis of genomic intervals with Bioconductor


Bioconductor version: Release (3.18)

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.

Author: Kristyna 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]

Maintainer: Kristyna Kupkova <kristynakupkova at gmail.com>

Citation (from within R, enter citation("GenomicDistributions")):

Installation

To install this package, start R (version "4.3") and enter:


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

BiocManager::install("GenomicDistributions")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomicDistributions")
1. Getting started with GenomicDistributions HTML R Script
2. Full power GenomicDistributions HTML
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Coverage, DataRepresentation, FunctionalGenomics, GenomeAnnotation, GenomeAssembly, Sequencing, Software, Visualization
Version 1.10.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License BSD_2_clause + file LICENSE
Depends R (>= 4.0), IRanges, GenomicRanges
Imports data.table, ggplot2, reshape2, methods, utils, Biostrings, plyr, dplyr, scales, broom, GenomeInfoDb, stats
System Requirements
URL http://code.databio.org/GenomicDistributions
Bug Reports http://github.com/databio/GenomicDistributions
See More
Suggests AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData
Linking To
Enhances BSgenome, extrafont, ensembldb, GenomicFeatures
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GenomicDistributions_1.10.0.tar.gz
Windows Binary GenomicDistributions_1.10.0.zip (64-bit only)
macOS Binary (x86_64) GenomicDistributions_1.10.0.tgz
macOS Binary (arm64) GenomicDistributions_1.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicDistributions
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicDistributions
Bioc Package Browser https://code.bioconductor.org/browse/GenomicDistributions/
Package Short Url https://bioconductor.org/packages/GenomicDistributions/
Package Downloads Report Download Stats