To install the package

Build from the source

devtools::build()
devtools::install()

Pre-requisite

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.

Install from the github repo

devtools::github_install('kharchenkolab/slideseqde/')

Introduction

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]