stream-trajectory-data-formatting

Reconstruct peak matrix export for STREAM compatibility via exportPeakMatrixForSTREAM

Summary

Export a peak-by-cell matrix from ArchR in a format compatible with STREAM trajectory analysis tool. This skill enables interoperability between ArchR's scATAC-seq processing and STREAM's trajectory inference, allowing users to leverage STREAM's visualization and analysis capabilities on ArchR-processed peak data.

When to use

Use this skill when you have completed peak calling and cell annotation in ArchR and want to perform trajectory inference or visualization in STREAM. Apply it specifically when your analysis goal requires STREAM's specialized trajectory reconstruction methods (e.g., elastic principal graphs, branching structure inference) on single-cell ATAC-seq peak data.

When NOT to use

• If your downstream trajectory tool is monocle3 or Slingshot — ArchR directly supports these via getMonocleTrajectories and addSlingShotTrajectories, without export overhead.
• If you need to preserve full dimensionality reduction or embedding information — STREAM export focuses only on the peak matrix; trajectory-specific embeddings from ArchR are not exported.
• If your peak matrix is already in a STREAM-compatible format from another source — re-exporting introduces redundant processing.

Inputs

• ArchR project object (processed with peak calls and cell annotations)
• Peak-by-cell accessibility matrix (internal ArchR representation)

Outputs

• Peak-by-cell matrix in CSV or TSV format compatible with STREAM
• Matrix with peaks as rows and cells as columns

How to apply

Load a processed ArchR project object containing peak calls and cell annotations. Call the exportPeakMatrixForSTREAM function on the ArchR project to generate a peak-by-cell matrix formatted for STREAM compatibility. The function produces output in CSV or TSV format that conforms to STREAM's expected matrix structure (peaks as rows, cells as columns, binary or accessibility values as matrix entries). Write the resulting matrix to a file and validate that the output dimensions match your peak and cell counts before importing into STREAM. The export preserves the peak-level and cell-level metadata necessary for downstream trajectory analysis.