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

# install devtools if necessary

# install bseqsc

# load

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 It is released under the Stanford Non-Commercial License.

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

  1. Got to
  2. Register and log in
  3. Download the latest R source code from the Download section.
  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: