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BRGenomics

Efficient tools for the analysis of high-resolution genomics data in R.

Explore the documentation: https://mdeber.github.io/

Installation

As of Bioconductor 3.11 (release date April 28, 2020), BRGenomics can be installed directly from Bioconductor:

# install.packages("BiocManager")
BiocManager::install("BRGenomics")

Alternatively, the latest development version can be installed from GitHub:

# install.packages("remotes")
remotes::install_github("mdeber/BRGenomics@R3")

BRGenomics (and Bioconductor 3.11) require R version 4.0 (release April 24, 2020). Installing the R3 branch, as shown above, can be installed under R >= 3.5

If you install the development version from Github and you’re using Windows, Rtools for Windows is required.

Features

See the documentation website, which includes an introductory vignette, as well as the documentation for currently implemented functions, complete with demonstrative example code. The package currently includes example PRO-seq data[1].

Limitations for Windows users

  • No support for parallel/multicore processing
  • No support for import bigWig files

To Do

  • Convert several functions into S4 generics
    • Note that in future versions, the names of the first argument of certain functions may change, but their order/utility will not. I.e., functions with with the first argument dataset.gr may become x
  • Formalize support for GRangesList objects (progress underway)
  • Write methods for BigWigFile/BigWigFileList objects (to avoid loading data into memory)
  • (Possibly) use GPos objects by default
  1. Hojoong Kwak, Nicholas J. Fuda, Leighton J. Core, John T. Lis (2013). Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing. Science 339(6122): 950–953. https://doi.org/10.1126/science.1229386