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SCENIC+ R → Python Data Handoff

Export R-based SCENIC+ data structures for import into Python pycisTopic workflows.

1|Updated Nov 20, 2025
Search Tags:#python#r#anndata#scenic+#cistopic#data-bridging#pycistopic
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill scenic-r-python-data-handoff
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: SCENIC+ R → Python Data Handoff
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/scenic-r-python-interop
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill scenic-r-python-data-handoff

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Bridges SCENIC+ data workflows between R-based SCENIC+ analyses and Python-based SCENIC+ pipelines to hand off data structures and metadata.

Core Features & Use Cases

  • Cross-language export and import of count matrices, region coordinates, fragment paths, and harmonized metadata from Seurat/Signac/ArchR in R to Python objects and pipelines.
  • End-to-end SCENIC+ workflow bridging: move preprocessing steps to Python and continue with pycisTopic, motif enrichment, and GRN inference.
  • Practical scenarios:
    • Scenario A: Signac → pycisTopic count matrix export and Python import.
    • Scenario B: ArchR → pycisTopic export and import.
    • Scenario C: cisTopic R → Python bridge.
    • Scenario D: Use of an existing peak atlas to skip peak calling.
    • Scenario E: Preserve RNA raw counts and produce AnnData for SCENIC+.

Quick Start

Export your Seurat/Signac objects from R using the described export steps, then import them in Python to initialize a pycisTopic CistopicObject and continue SCENIC+ analysis.

Frequently Asked Questions about SCENIC+ R → Python Data Handoff

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I export a Seurat object to Python for SCENIC+ analysis?▼

Export raw counts, region coordinates, fragment paths, and harmonized metadata from your Seurat object in R, then import them in Python to initialize a pycisTopic CistopicObject and continue SCENIC+ analysis.

Can I bridge ArchR objects to pycisTopic workflows?▼

Yes, ArchR to pycisTopic export and import is supported, allowing you to transfer count matrices and fragment paths from R to Python to continue SCENIC+ analysis.

What is the best way to transition cisTopic R objects to Python?▼

The cisTopic R to Python bridge transfers count matrices and harmonized metadata into Python objects, enabling direct continuation of SCENIC+ analysis.

Does SCENIC+ data bridging preserve RNA raw counts for AnnData?▼

Yes, SCENIC+ data bridging preserves RNA raw counts and produces AnnData objects by exporting raw counts and harmonized metadata from R to Python.

How do I skip peak calling when moving SCENIC+ data from R to Python?▼

To skip peak calling when moving SCENIC+ data from R to Python, use an existing peak atlas during the pycisTopic import process.

What metadata is required for Signac to pycisTopic count matrix export?▼

Signac to pycisTopic count matrix export requires raw counts, region coordinates, fragment paths, and harmonized metadata to ensure data fidelity.

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