stPipe

The stPipe package provides a comprehensive pipeline for preprocessing sequencing-based spatial transcriptomics data, including 10X Visium, BGI Stereo-seq, Slide-seq, and Curio-seeker.

Installation

From Bioconductor (recommended approach)

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("stPipe")

From GitHub (Developmental version)

if (!require("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("mritchielab/stPipe")

or

if (!require("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("mritchielab/stPipe")

The sample data is downsampled from a 10X Visium mouse spleen sample (Sample 709). It is a probe-based, FFPE tissue dataset generated from paired-end FASTQ files. The data can be downloaded from Zenodo, and a detailed sample description is available in the SpatialBench paper.

Sample HTML report for demo data can be found here.