README.md

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

| Master | Dev | |--------|-----| | | |

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:

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

Or from GitHub:

devtools::install_github("databio/GenomicDistributions")

Data package

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 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. 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

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.