https://github.com/databio/genomicdistributions
Calculate and plot distributions of genomic ranges
https://github.com/databio/genomicdistributions
Last synced: 10 months ago
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Calculate and plot distributions of genomic ranges
- Host: GitHub
- URL: https://github.com/databio/genomicdistributions
- Owner: databio
- License: other
- Created: 2018-02-05T22:54:09.000Z (over 8 years ago)
- Default Branch: devel
- Last Pushed: 2025-04-23T19:48:14.000Z (about 1 year ago)
- Last Synced: 2025-04-23T20:35:28.185Z (about 1 year ago)
- Language: R
- Homepage: http://code.databio.org/GenomicDistributions
- Size: 9.28 MB
- Stars: 26
- Watchers: 15
- Forks: 10
- Open Issues: 11
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS
- License: LICENSE
Awesome Lists containing this project
README
| Master | Dev |
|--------|-----|
|[](https://travis-ci.org/databio/GenomicDistributions) | [](https://travis-ci.org/databio/GenomicDistributions) |
# GenomicDistributions
An R package that provides functions for 1) calculating and 2) visualizing a variety of statistics for a collection of genomic ranges. If you have a set of genomic ranges, such as a BED file the GenomicDistributions R package can help you to explore, annotate, visualize,and compare it.
## Installing
### Main package
With Bioconductor:
```r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicDistributions")
```
Or from GitHub:
```r
devtools::install_github("databio/GenomicDistributions")
```
### Data package
[GenomicDistributionsData](https://github.com/databio/GenomicDistributionsData): includes full data files, too large to include in GenomicDistributions
## Quick start
See the vignettes for more information: http://code.databio.org/GenomicDistributions
## Building long vignettes
In the [long_vignettes](/long_vignettes) are vignettes that require large external data and take a long time to run. Therefore, they should be pre-built. You can render them manually by running [long_vignettes/render-long-vignettes.R](long_vignettes/render-long-vignettes.R). This will use `knitr` to run the vignette and put the result into the `vignettes` folder, along with output figures.
**Cite GenomicDistributions:**\
Kupkova K., Mosquera J.V., Smith J.P., Stolarczyk M, Danehy T., Lawson J.T., Rogers S., LeRoy N., Sheffield N.C. GenomicDistributions: fast analysis of genomic intervals with Bioconductor. *BMC Genomics* 23, 299 (2022). https://doi.org/10.1186/s12864-022-08467-y