Create a new RStudio project

Open RStudio and create a new project, for more info see Using-Projects:

File > New Project > New Directory > New Project

Name the new directory (e.g. Spatial_transcriptomics), and check “use renv with this project” if present.

Learn more about renv.

Install packages

One of R’s many benefits is the large, active user community, which produces and maintains many packages that extend the functionality of base R and provide functions that enable bioinformatic analyses without completely custom code.

The following package installation commands should be run individually, in the R console. Many of them will require your input to determine which, if any, dependencies should be updated; for the quickest result, attempt ‘n’ (none) first.

R-universe for arm64 installations

r-universe is a new umbrella project by rOpenSci. It uses cross-compiling for arm64 binaries.

For those who are using Macs that have M1/M2/M3 chips, if you have trouble installing the packages and get error that is similar to “ld: warning: ignoring file ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib’: found architecture ‘arm64’, required architecture ‘x86_64’”, please go to https://r-universe.dev/search/ and search for the packages and use the installation instructions provided there.

BiocManager

BiocManager is an interface for the bioinformatics-specific R package repository. We will be using BiocManager to install other packages when possible, rather than the base R function install.packages.

if (!requireNamespace("BiocManager", quietly = TRUE)){
    install.packages("BiocManager")
}

rmarkdown

The rmarkdown package, when used with others like tinytex and knitr, allows you to knit your Rmd document to nicely-formatted reports.

if (!any(rownames(installed.packages()) == "rmarkdown")){
  BiocManager::install("rmarkdown")
}
library(rmarkdown)

tinytex

TinyTeX is a small LaTeX distribution for use with R.

if (!any(rownames(installed.packages()) == "tinytex")){
  BiocManager::install("tinytex")
}
library(tinytex)

knitr

if (!any(rownames(installed.packages()) == "knitr")){
  BiocManager::install("knitr")
}
library(knitr)

kableExtra

The kableExtra package gives the user fine-grained control over table formats. This is useful for knit reports.

if (!any(rownames(installed.packages()) == "kableExtra")){
  BiocManager::install("kableExtra")
}
library(kableExtra)

ggplot2

An extremely popular package by the authors of RStudio, ggplot2 produces highly customizable plots.

if (!any(rownames(installed.packages()) == "ggplot2")){
  BiocManager::install("ggplot2")
}
library(ggplot2)

dplyr

Like ggplot2 and tidyr, dplyr is part of the “tidyverse” by the RStudio authors: a group of packages designed for data analysis and visualization.

if (!any(rownames(installed.packages()) == "dplyr")){
  BiocManager::install("dplyr")
}
library(dplyr)

tidyr

if (!any(rownames(installed.packages()) == "tidyr")){
  BiocManager::install("tidyr")
}
library(tidyr)

viridis

viridis produces accessible color palettes.

if (!any(rownames(installed.packages()) == "viridis")){
  BiocManager::install("viridis")
}
library(viridis)

hdf5r

HDF5 (heirarchical data format version five) files can be used to store single cell expression data (including output from Cell Ranger). The hdf5r package provides utilities for interacting with the format.

if (!any(rownames(installed.packages()) == "hdf5r")){
  BiocManager::install("hdf5r")
}
library(hdf5r)

Seurat

Seurat is an extensive package for the analysis of single cell experiments, from normalization to visualization.

if (!any(rownames(installed.packages()) == "Seurat")){
  BiocManager::install("Seurat")
}
library(Seurat)

sf

sf is a package that supports simple features, a standardized way to encode spatial vector data.

if (!any(rownames(installed.packages()) == "ComplexHeatmap")){
  install.packages("sf")
}

ComplexHeatmap

ComplexHeatmap produces beautiful, highly-customizable heat maps.

if (!any(rownames(installed.packages()) == "ComplexHeatmap")){
  BiocManager::install("ComplexHeatmap")
}
library(ComplexHeatmap)

biomaRt

This package provides an interface to Ensembl databases.

if (!any(rownames(installed.packages()) == "biomaRt")){
  BiocManager::install("biomaRt")
}
library(biomaRt)

limma

Originally developed for microarray data, limma provides functions for linear modeling and differential expression.

if (!any(rownames(installed.packages()) == "limma")){
  BiocManager::install("limma")
}
library(limma)

remotes

Some packages (or versions of packages) cannot be installed through Bioconductor. The remotes package contains tools for installing packages from a number of repositories, including GitHub.

if (!any(rownames(installed.packages()) == "remotes")){
  utils::install.packages("remotes")
}
library(remotes)

NicheDE

NicheDE performs niche-differential gene expression analysis, i.e. tests if the expression of a given cell type is influenced by being spatially close to another celltype.

if (!any(rownames(installed.packages()) == "NicheDE")){
  options(timeout=9999999)
  remotes::install_github("kaishumason/nicheDE")
}
library(nicheDE)

spacexr

spacexr implements computations methods for cell type identification and differential expression on spatial transcriptomics datasets.

## may need to modify the download time out limit for the installation to be successful
#options(timeout = 600000000)
if (!any(rownames(installed.packages()) == "spacexr")){
remotes::install_github("dmcable/spacexr", build_vignettes = FALSE)
}

scCustomize

scCustome is a package with collection of functions created and/or curated to aid in visualization and analysis of single-cell data in R

if (!any(rownames(installed.packages()) == "scCustomize")){
  utils::install.packages("scCustomize")
}
library(scCustomize)

ape

Analysis of Phylogenetics and Evolution (ape) is used to generate and manipulate phylogenetic trees. In this workshop, we will be using ape to investigate the relationships between clusters.

if (!any(rownames(installed.packages()) == "ape")){
  utils::install.packages("ape")
}
library(ape)

openxlsx

The openxlsx package is a suite of tools for reading and writing .xlsx files.

if (!any(rownames(installed.packages()) == "openxlsx")){
  BiocManager::install("openxlsx")
}
library(openxlsx)

Verfiy installation

Finally, we can get the session info to ensure that all of the packages were installed and loaded correctly.

sessionInfo()

Download materials and prepare for the next section

In the R console run the following command to download part 1 of the workshop.

Markdown template document

download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2025-March-Spatial-Transcriptomics/main/data_reduction/01-Data_exploration.Rmd", "01-Datat_exploration.Rmd")