archr

ArchR: Single-Cell ATAC-Seq Analysis

Overview

ArchR is a powerful R package for analyzing single-cell ATAC-seq (Assay for Transposase-Accessible Chromatin sequencing) data. It provides a complete workflow from raw reads to interpretation, including dimensionality reduction, clustering, peak calling, motif analysis, and integration with gene expression data.

When to Use This Skill

This skill should be used when:

• Analyzing single-cell ATAC-seq data
• Performing chromatin accessibility analysis
• Identifying cell types based on chromatin state
• Finding regulatory elements and TF motifs
• Integrating scATAC-seq with scRNA-seq
• Creating pseudo-bulk accessibility tracks

Quick Start

Installation

# Install ArchR
install.packages("ArchR")

# Or from GitHub
devtools::install_github("GreenleafLab/ArchR", ref="master")

# Install dependencies
install.packages("BSgenome.Hsapiens.UCSC.hg38")

Basic Setup

library(ArchR)
library(ggplot2)
library(dplyr)

# Set genome
addArchRGenome("hg38")

Creating ArchR Project

From Fragments

# Create input files
inputFiles <- c(
  "sample1" = "path/to/sample1.fragments.tsv.gz",
  "sample2" = "path/to/sample2.fragments.tsv.gz"
)

# Create Arrow files
ArrowFiles <- createArrowFiles(
  inputFiles = inputFiles,
  sampleNames = names(inputFiles),
  filterTSS = 4,          # Minimum TSS enrichment
  filterFrags = 1000,     # Minimum fragments
  addTileMat = TRUE,      # Add tile matrix
  addGeneScoreMat = TRUE  # Add gene score matrix
)

# Create ArchR project
proj <- ArchRProject(
  ArrowFiles = ArrowFiles,
  outputDirectory = "ArchR_Project"
)

Analysis Workflow

Dimensionality Reduction

# Add dimensionality reduction
proj <- addIterativeLSA(
  ArchRProj = proj,
  useMatrix = "TileMatrix",
  name = "IterativeLSI",
  clusterParams = list(
    resolution = c(0.2, 0.4, 0.8),
    sampleCells = 10000,
    n.start = 10
  )
)

Clustering

# Add clusters
proj <- addClusters(
  input = proj,
  reducedDims = "IterativeLSI",
  method = "Seurat",
  name = "Clusters",
  resolution = 0.8
)