GenomicDistributions

DOI: 10.18129/B9.bioc.GenomicDistributions    

This is the development version of GenomicDistributions; to use it, please install the devel version of Bioconductor.

Produces Summaries and Plots of Features Distributed Across Genomes

Bioconductor version: Development (3.13)

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: Nathan C. Sheffield [aut], Kristyna Kupkova [aut, cre], Jose Verdezoto [aut], Tessa Danehy [ctb], John Lawson [ctb], Jose Verdezoto [ctb], Michal Stolarczyk [ctb], Jason Smith [ctb]

Maintainer: Kristyna Kupkova <kristynakupkova at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 0.99.4
In Bioconductor since BioC 3.13 (R-4.1)
License BSD_2_clause + file LICENSE
Depends R (>= 4.0), IRanges, GenomicRanges
Imports data.table, ggplot2, reshape2, methods, utils, Biostrings
LinkingTo
Suggests AnnotationFilter, rtracklayer, testthat, knitr, BiocStyle, rmarkdown
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_0.99.4.tar.gz
Windows Binary GenomicDistributions_0.99.4.zip (32- & 64-bit)
macOS 10.13 (High Sierra) GenomicDistributions_0.99.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicDistributions
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicDistributions
Package Short Url https://bioconductor.org/packages/GenomicDistributions/
Package Downloads Report Download Stats

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