Installation

stGrads is an R package for analyzing and visualizing spatial transcriptomics data (10x Visium / 10x HD / STO and even user-defined multi-omics data).
This page shows how to install it and verify the setup.

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Requirements

• R: 4.1 or newer is recommended

• OS: macOS / Linux / Windows

• (Optional) R packages for tutorials: Seurat (v5+), ggplot2, patchwork, data.table

If you install from source on Windows/macOS, you may need basic build tools:

• Windows: Rtools (matching your R version)

• macOS: Xcode Command Line Tools (xcode-select --install)

• Linux: common build essentials (e.g., build-essential)

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Install the development version

# 1) If you don't have remotes yet:
install.packages("remotes")

# 2) Install stGrads from GitHub:
remotes::install_github("yifanfu01/stGrads")

# 3) Load the package:
library(stGrads)

# 4) Quick check:
packageVersion("stGrads")

Tip: To update later, just run the same install_github() command again.

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(Optional) Install common dependencies for the tutorials

install.packages(c(
  "Seurat",      # main analysis framework (v5+)
  "ggplot2",     # plotting
  "patchwork",   # plot layout
  "data.table"   # fast data handling
))

Install from a local clone (advanced)

If you have cloned the repository locally:

# Using remotes:
remotes::install_local("yifanfu01/stGrads")

# Or from terminal:
# R CMD build yifanfu01/stGrads
# R CMD INSTALL stGrads_<version>.tar.gz