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
| Maintainer | Kristyna Kupkova <kristynakupkova@gmail.com> |
| 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] |
| License | BSD_2_clause + file LICENSE |
| URL | http://code.databio.org/GenomicDistributions |
| Bug Reports | http://github.com/databio/GenomicDistributions |
| Downloads rank | 317 |
| Source branch | RELEASE_3_23 |
| biocViews | Coverage, DataRepresentation, FunctionalGenomics, GenomeAnnotation, GenomeAssembly, Sequencing, Software, Visualization |
Documentation
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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