GenomicDistributions
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
Bioconductor version: Release (3.20)
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("GenomicDistributions")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, DataRepresentation, FunctionalGenomics, GenomeAnnotation, GenomeAssembly, Sequencing, Software, Visualization |
| Version | 1.14.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3.5 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | GenomicDistributions_1.14.0.zip |
| macOS Binary (x86_64) | GenomicDistributions_1.14.0.tgz |
| macOS Binary (arm64) | GenomicDistributions_1.13.0.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 |