archr - Analyze scATAC-seq data with ArchR in R
Runs R-based scATAC-seq workflows including Arrow files, dimensionality reduction, clustering, gene scores, peak calling, motif analysis, chromVAR, footprinting, integration, and trajectories.
Tags
Updated: 2026-10-01Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Create Arrow files
- Infer doublets
- Run iterative LSI
- Apply Harmony correction
- Cluster cells
- Generate UMAP embeddings
- Compute gene scores
- Call MACS2 peaks
- Find marker peaks
- Perform motif enrichment
- Calculate chromVAR deviations
- Analyze TF footprints
- Transfer scRNA-seq labels
- Analyze trajectories
- Visualize genome tracks
Inputs
- Fragment files
- BAM files
- Reference genome
- scRNA-seq reference
- Cell-type labels
- Multiome preprocessing outputs
- Analysis parameters
Outputs
- Arrow files
- ArchRProject objects
- Cell embeddings
- Cell clusters
- Gene score matrices
- Peak matrices
- Marker features
- Motif enrichments
- chromVAR deviation matrices
- TF footprints
- Transferred cell labels
- Trajectory analyses
- Genome track plots
- PDF reports
Requirements
- R >= 4.0
- Bioconductor dependencies
- ArchR and extra packages
- MACS2 for peak calling
- Seurat for scRNA-seq integration
- cellranger-arc for multiome preprocessing
- Sufficient system memory