ArchR Documentation

ArchR provides pre-compiled Docker images based on rocker/rstudio that include ArchR and all necessary dependencies.

To run an interactive RStudio instance:

1. Pull the greenleaflab/archr:latest image.
2. Run the container, mapping your local workspace to /workspace and exposing port 8787.
3. Access RStudio via localhost:<your_port_of_interest>.

To run an interactive bash console instead of RStudio, replace the command with bash.

# Pull the latest image
docker image pull greenleaflab/archr:latest

# Run RStudio container
docker run -it --rm -v <your_workspace>:/workspace -p <your_port_of_interest>:8787

# Run interactive bash console instead
docker run -it --rm -v <your_workspace>:/workspace -p <your_port_of_interest>:8787 bash

You can use renv to create a reproducible environment. ArchR provides lock files for specific R versions. Supported R versions are 4.4 and 4.1.

To use this method:

1. Install and load renv.
2. Create and set a project directory.
3. Download the appropriate renv.lock file for your R version.
4. Run renv::init() to bootstrap the environment.

# Setup renv
install.packages("renv")
library(renv)

# Create project directory
dir.create(path = "./<project_name>", showWarnings = FALSE)
setwd("./<project_name>")

# Download lock file (Choose based on your R version)
# For R 4.4:
download.file(url = "https://pub-9ae435458ecc412abbbc9420a502ec38.r2.dev/renv.lock", destfile = "./renv.lock")

# For R 4.1:
# download.file(url = "https://pub-9ae435458ecc412abbbc9420a502ec38.r2.dev/renv_4_1.lock", destfile = "./renv.lock")

# Initialize environment
renv::init()

To install ArchR directly in an R session, follow these steps in order. Ensure you install devtools and BiocManager first to handle GitHub and Bioconductor dependencies. After installing the ArchR package, you must run ArchR::installExtraPackages() to install any remaining dependencies required for full functionality.

# 1. Install devtools
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")

# 2. Install BiocManager
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

# 3. Install ArchR from GitHub
devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())

# 4. Install extra dependencies
library(ArchR)
ArchR::installExtraPackages()

ArchR provides direct support for trajectory analysis using monocle3 and Slingshot. Key functions include:

• getMonocleTrajectories: Retrieve monocle3 trajectories.
• addMonocleTrajectory: Add monocle3 trajectories to the ArchR object.
• addSlingShotTrajectories: Add Slingshot trajectories to the ArchR object.

ArchR supports integrated analysis of paired scATAC-seq and scRNA-seq data using the following functions:

• importFeatureMatrix: Import feature matrices.
• addGeneExpressionMatrix: Add gene expression data.
• addIterativeLSI: Perform Iterative LSI.
• addCombinedDims: Add combined dimensions.