About

scphaser is an R package for haplotype phasing using single-cell RNA-seq data.

scphaser is available free to use under the GNU GPL version 3 license.

Installation

scphaser is available at the R package repository CRAN and can be installed by:

source("http://www.bioconductor.org/biocLite.R")
biocLite("BiocParallel")
install.packages('scphaser')

Installation of the development version can be done via the devtools package:

library('devtools')
devtools::install_github('edsgard/scphaser')

Tutorial

Once you've installed scphaser you will be able to follow the vignette-tutorial. You can open it by:

vignette('scphaser')

Minimal example

library('scphaser')
data(marinov)
acset = new_acset(featdata = marinov[['featdata']], refcount = marinov[['refcount']],
	altcount = marinov[['altcount']], phenodata = marinov[['phenodata']])
acset = call_gt(acset)
acset = filter_acset(acset)
acset = phase(acset)
head(acset[['phasedfeat']])

Function reference manual

To get help for specific functions you can use ?fcn, for example:

library('scphaser')
?phase

The complete function reference manual for all functions can be found at "doc/refman.pdf" within the installed library directory. You can also view the latest version by:

browseURL('https://github.com/edsgard/scphaser/tree/master/inst/doc/refman.pdf')

Citation

If you use scphaser, please cite it as follows:

Edsgärd D. et al., scphaser: Haplotype Inference Using Single-Cell RNA-Seq Data, Bioinformatics, 2016
DOI: 10.1093/bioinformatics/btw484