iSpatial: infer spatial transcriptome

infer and enhance probe-based spatial transcriptome by intergrating with scRNA-seq

Rationale:

• For Probe-based spatial transcriptome (such as: merFISH, STARmap, seqFISH):
  • target few genes
  • with spatial information of all cells
• For single cell RNA-seq:
  • detect all genes
  • with out spatial information

• After infer: transcriptome-wide spatial expression
  • all genes
  • with spatial information

Methodology:

Installation:

# This package based on Seurat and harmony.
# You can find more in:
# https://satijalab.org/seurat/articles/install.html
# https://github.com/immunogenomics/harmony
install.packages(c('Seurat', "harmony"))

install.packages("devtools") # if you have not installed "devtools" package
devtools::install_github("Czh3/iSpatial")

Sample Datasets:

library(iSpatial)

# scRNA-seq data
data(NA_scRNA)

# merFISH data
data(NA_merFISH)

Usage:

NA_merFISH_infer = infer_v2(NA_merFISH, NA_scRNA)

Output:

A Seurat object: Inferred expresstion matrix is stored in "enhanced" assay.

Tutorial:

For step by step usage, see:

• Mouse striatum example.
• Mouse cortex example.