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pycistopic-atac-topic-modeling

Identify co-accessible regulatory programs in scATAC-seq data using LDA topic modeling.

1|Updated Nov 20, 2025
Search Tags:#topic-modeling#lda#scatac-seq#scenic-plus#motif-enrichment#pycistopic#region-sets
One-click install
npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill pycistopic-atac-topic-modeling
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pycistopic-atac-topic-modeling
Source: https://github.com/tony-zhelonkin/SciAgent-toolkit/tree/main/skills/pycistopic-atac-topic-modeling
Command: npx skills add https://github.com/tony-zhelonkin/SciAgent-toolkit --skill pycistopic-atac-topic-modeling

SYSTEM DOCUMENTATION & REQUIREMENTS

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+.

Frequently Asked Questions about pycistopic-atac-topic-modeling

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

FAQPage Schema
How do I identify co-accessible regulatory programs in scATAC-seq data?▼

LDA-based topic modeling with pycisTopic identifies co-accessible regulatory programs in scATAC-seq data by applying MALLET to generate binarized topics and region sets.

What's the best way to prepare scATAC-seq region sets for motif enrichment?▼

Generating region_sets BED files through pseudobulk generation, peak calling, and consensus peaks with pycisTopic provides the input needed for motif enrichment.

Do I need MALLET to run pycisTopic for scATAC-seq topic modeling?▼

Yes, MALLET is required to run pycisTopic for scATAC-seq topic modeling because the LDA-based identification of co-accessible regulatory programs depends directly on it.

Can I use pycisTopic region sets for SCENIC+ regulatory network analysis?▼

Yes, pycisTopic region_sets BED files and binarized topics integrate directly with pycistarget and SCENIC+ to construct downstream regulatory networks.

How does LDA topic modeling work on scATAC-seq data?▼

LDA topic modeling on scATAC-seq data groups co-accessible regulatory regions into latent topics, enabling identification of regulatory programs that define cell states.

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