GenomicDistributions

DOI: 10.18129/B9.bioc.GenomicDistributions  

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	Coverage, DataRepresentation, FunctionalGenomics, GenomeAnnotation, GenomeAssembly, Sequencing, Software, Visualization
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 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
LinkingTo
Suggests	AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown, GenomicDistributionsData
SystemRequirements
Enhances	BSgenome, extrafont, ensembldb, GenomicFeatures
URL	http://code.databio.org/GenomicDistributions
BugReports	http://github.com/databio/GenomicDistributions
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	GenomicDistributions_1.6.0.tar.gz
Windows Binary	GenomicDistributions_1.6.0.zip
macOS Binary (x86_64)	GenomicDistributions_1.6.0.tgz
macOS Binary (arm64)	GenomicDistributions_1.6.0.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