BSeq-sc is implemented as an
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)
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:
bseqscby 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/bseqscsub-directory in the user's home directory for subsequent usage:
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