# BSeq-sc: Deconvolution of Bulk Sequencing Experiments using Single Cell Data

`BSeq-sc` is a bioinformatics analysis pipeline that leverages single-cell sequencing data
to estimate cell type proportion and cell type-specific gene expression differences from  
RNA-seq data from bulk tissue samples.


![Bseq-SC pipeline](vignettes/images/pipeline.resized.png)

## How to cite `BSeq-sc`
When using this work in any way, please cite the following publication:

> *A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure*<br />
> <small>M. Baron, A. Veres, S.L. Wolock, A. L. Faust, R. Gaujoux, A. Vetere, J. Hyoje Ryu, B. K. Wagner, S. Shen-Orr, A. M. Klein, D. A. Melton, I. Yanai<br /></small>
> Cell Systems. 2016 Oct 26 [10.1016/j.cels.2016.08.011](https://www.ncbi.nlm.nih.gov/pubmed/27667365) 

## Installation
```R
# install devtools if necessary
install.packages('devtools')

# install the bseqsc package
devtools::install_github('shenorrlab/bseq-sc')

# load
library(bseqsc)
```

## More information
  
  * [Detailed installation instructions](http://shenorrlab.github.io/bseqsc/vignettes/pages/installation.html)
  * [Sample analysis](http://shenorrlab.github.io/bseqsc/vignettes/bseq-sc.html)
  * [Documentation](http://shenorrlab.github.io/bseqsc/reference/index.html)

