An R-package for breakpoint detection in single cell Strand-seq data.

Collaborators: David Porubsky, Ashley D. Sanders, Aaron Taudt

Installation

Stable bioconductor version

To install the current stable version from Bioconductor, please visit http://bioconductor.org/packages/breakpointR/

Development version from Github

To install the development version from Github, follow the steps given below. The installation has only been tested on Ubuntu so far, if you need to install on Windows or Mac additional steps might be necessary (e.g. installation of Rtools from https://cran.r-project.org/bin/windows/Rtools/)

1. Install a recent version of R (>=3.5.0) from https://www.r-project.org/

2. Optional: For ease of use, install Rstudio from https://www.rstudio.com/

3. Open R and install all dependencies. Please ensure that you have writing permissions to install packages. Execute the following lines one by one:

   To install required packages

   if (!requireNamespace(“BiocManager”, quietly=TRUE)) install.packages(“BiocManager”) install(“GenomicRanges”) install(“GenomicAlignments”) install.packages(“devtools”) library(devtools)

4. To install breakpointR package from github

   Option1

   install_github(“daewoooo/breakpointRdata”, force=TRUE)
   install_github(“daewoooo/breakpointR”, force=TRUE)

   Option2

   install_git(“git://github.com/daewoooo/breakpointRdata.git”, branch = “master”)
   install_git(“git://github.com/daewoooo/breakpointR.git”, branch = “master”)

How to use breakpointR

Please refert to the vignette for tutorials on all breakpointR features.

Report Errors

If you encounter errors of any kind, please report an issue here.

NOTE

The breakpointR package is currently under development and contains unpublished work. Any usage for publishing is strictly prohibited without permission.