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/)
Run StrandPhaseR: strandPhaseR(inputfolder = , outputfolder = , positions = , WCregions = , chromosomes = ) or use config file as follows strandPhaseR(inputfolder = , outputfolder = , positions = , WCregions = , configfile = )
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The developemtal (branch ‘devel’) version of StrandPhaseR includes recent unpublished work.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.
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/)
Install a recent version of R (>=3.3.0) from https://www.r-project.org/
Optional: For ease of use, install Rstudio from https://www.rstudio.com/
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)
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
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.