pycistopic-atac-topic-modeling
CommunityDiscover ATAC regulatory programs via topics
Authortony-zhelonkin
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Topic modeling on scATAC-seq data to identify co-accessible regulatory region programs using MALLET-based LDA, enabling downstream motif enrichment and SCENIC+ workflows.
Core Features & Use Cases
- Identify co-accessible regulatory programs in scATAC data with LDA-based topic modeling.
- Produce region_sets BED files for motif enrichment and downstream SCENIC+ analyses.
- Integrate with downstream pycistarget and SCENIC+ to construct regulatory networks.
Quick Start
Run a minimal workload on a sample scATAC dataset to generate region_sets and binarized topics for SCENIC+.
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
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Please help me install this Skill: Name: pycistopic-atac-topic-modeling Download link: https://github.com/tony-zhelonkin/SciAgent-toolkit/archive/main.zip#pycistopic-atac-topic-modeling Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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