BSeq-sc is implemented as an R package, bseqsc, which can be installed from GitHub by:

# install devtools if necessary
install.packages('devtools')

# install bseqsc
devtools::install_github('shenorrlab/bseqsc')

library(bseqsc)

## External dependency

BSeq-sc uses CIBERSORT to estimate cell type proportions, based on reference expression profiles.

Due to licensing requirements, source code for this algorithm needs to be downloaded separately from its website http://cibersort.stanford.edu. It is released under the Stanford Non-Commercial License.

In order to use it with bseqsc you will need to:

1. Got to http://cibersort.stanford.edu
4. Configure bseqsc by pointing it to the downloaded file. This is done using the function bseqsc_config, which will copy the given R source file into the R-data/bseqsc sub-directory in the user’s home directory for subsequent usage:
bseqsc_config('path/to/downloaded/source/CIBERSORT.R')