Skills
.Work. You
Rest

SCENIC+ R → Python Data Handoff

Community

Seamless R↔Python SCENIC+ data handoff.

Data & Analytics#python#r#anndata#scenic+#cistopic#data-bridging#pycistopic
Authortony-zhelonkin
Version1.0.0
Installs0

System Documentation

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.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: SCENIC+ R → Python Data Handoff
Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#scenic-r-python-data-handoff

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
View Source Repository

Agent Skills Search Helper

Install a tiny helper to your Agent, search and equip skill from 471,000+ vetted skills library on demand.