In shenorrLab/bseqsc: Deconvolution of Bulk Sequencing Experiments using Single Cell Data

BSeq-sc is implemented as an R package, r BiocStyle::Githubpkg('shenorrlab', 'bseqsc'), which can be installed from GitHub by:

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

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

# load
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
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:

bseqsc_config('path/to/downloaded/source/CIBERSORT.R')

shenorrLab/bseqsc documentation built on May 29, 2019, 9:23 p.m.