devtools::build()
devtools::install()
The installation depends on the (RCTD)[https://github.com/dmcable/RCTD] package for initial deconvolution and annotation transfer from an existing scRNA-seq dataset. Install RCTD by following the instructions given in the linked repo.
devtools::github_install('kharchenkolab/slideseqde/')
The slideseqde package aims to find the differentially expressed genes
for a target cell-type in a "context" sensitive manner. While the context
depends on the biological question one sets out to ask and can vary, we
consider coherant spatial segments as contexts. Below is a graphical
outline of a typical slide-seq DE pipeline we propose. A more detailed
explanation can be obtained from the attached (vignette)[https://github.com/kharchenkolab/slideseqde/blob/master/vignettes/slideseqde.Rmd]
