SPADE

Spatial Deconvolution for Domain Specific Cell-type Estimation

SPADE, a reference-based approach, harnesses the power of single-cell RNA sequencing data, spatial location details, and histological information to accurately estimate the proportions of various cell types at each spatial location. A crucial characteristic of SPADE is its ability to account for cell type sparsity across locations, thereby enabling the identification of cell types prior to proportion estimation.

Installation

Dependencies

• R version >= 4.0.0.
• R packages: Biobase, caret, glmnet, tidyverse, NOISeq, EBImage, rlist, alabama

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

# install the SPADE package
devtools::install_github('anlingUA/SPADE')

# load
library(SPADE)

• The first step of SPADE utilizes spaGCN to cluster locations into domains. To get the identified spatial domain of your data, refer to the tutorial of spaGCN

• For an example how to use SPADE and the data used for the tutorial can be downloaded from here