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StrandPhaseR

R Package for phasing of single cell Strand-seq data

Collaborators: David Porubsky, Ashley D. Sanders

Installation

Bioconductor version (not available yet)

Under the development.

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 (>=3.3.0) 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 StrandPhaseR package from github

   To install published version of the package:

   install_github("daewoooo/StrandPhaseR")

   To install developmental version of the package:

   install_github("daewoooo/StrandPhaseR", ref = "devel")

How to use StrandPhaseR

1. Start Rstudio
2. Load StrandPhaseR package: library('StrandPhaseR')
3. Run StrandPhaseR: strandPhaseR(inputfolder = <input_folder>, outputfolder = <output_folder>, positions = <SNV_positions>, WCregions = <haplotypeInformative_WCregions>, chromosomes = ) or use config file as follows strandPhaseR(inputfolder = <input_folder>, outputfolder = <output_folder>, positions = <SNV_positions>, WCregions = <haplotypeInformative_WCregions>, configfile = <config_file>)

More information on how to use StrandPhaseR for phasing can be found here.

Report Errors

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

NOTE

The developemtal (branch 'devel') version of StrandPhaseR includes recent unpublished work. To avoid any conflict of interest please consult usage for publication with the author.