archr-project-manipulation

ArchR Project Manipulation

Summary

Load, transform, and annotate single-cell ATAC-seq ArchR project objects using core functions like addIterativeLSI, addCombinedDims, and export routines. This skill enables reproducible manipulation of processed peak matrices and cell metadata for downstream trajectory and multimodal analysis.

When to use

You have a processed ArchR project object (containing peak calls, cell barcodes, and quality control metadata) and need to: (1) reduce dimensionality of the peak matrix via iterative LSI; (2) integrate multimodal data by combining ATAC and RNA dimensions; (3) prepare the peak matrix for export to external trajectory tools (Monocle3, Slingshot, STREAM); or (4) add gene expression matrices from paired scRNA-seq experiments.

When NOT to use

• Raw, unprocessed sequencing data (use ArchR QC functions first)
• If peak matrix has already been exported to another format and you do not need to re-integrate ArchR metadata or trajectory results
• If no paired scRNA-seq is available and gene expression integration is the sole goal

Inputs

• ArchR project object (processed, with peak calls and cell annotations)
• Optional: scRNA-seq feature matrix (gene × cell counts)
• Optional: trajectory analysis method selection (character: 'monocle3' or 'slingshot')

Outputs

• Modified ArchR project object (with LSI, combined dimensions, trajectory embedding, or gene expression matrix added)
• Peak-by-cell matrix file in STREAM-compatible format (CSV or TSV)
• Trajectory embedding coordinates (stored in ArchR project metadata)

How to apply

Load the ArchR project object in R. If you have a paired scRNA-seq dataset, use importFeatureMatrix to ingest gene expression counts, then addGeneExpressionMatrix to integrate into the ArchR project. Run addIterativeLSI on the peak matrix to compute iterative LSI dimensionality reduction, which produces latent semantic components suitable for visualization and downstream analysis. If integrating both ATAC and RNA modalities, use addCombinedDims to create a joint embedding. For trajectory analysis, conditionally invoke addMonocleTrajectory (Monocle3) or addSlingShotTrajectories (Slingshot) based on user selection. For export to STREAM, invoke exportPeakMatrixForSTREAM to write the peak-by-cell matrix in STREAM-compatible CSV or TSV format. Verify that the project object is returned with updated assays and metadata slots reflecting each operation.