skills.rest
CHENyiru3
CHENyiru3COMMUNITY
Explore all skills by this author →
GitHub

scribble

Integrate RNA, ATAC, and protein data into joint embeddings for single-cell analyses.

Updated Apr 19, 2026
Search Tags:#integration#embeddings#single-cell#scRNA-seq#protein#multi-omics#atac
One-click install
npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill scribble
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scribble
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/multiomics/integration-tools/scribble
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill scribble

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Scribble enables seamless integration of multiple single-cell modalities (RNA, ATAC, and protein) to produce unified representations for downstream analyses.

Core Features & Use Cases

  • Integrates RNA, ATAC, and protein data into joint embeddings.
  • Supports a range of integration strategies (CCA, WNN, etc.) and batch correction.
  • Use cases include cross-modality alignment, multi-omics data fusion, and comparative analyses across conditions.

Quick Start

Install scribble and run a simple multi-omics integration on your single-cell datasets to obtain a unified embedding.

Frequently Asked Questions about scribble

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

FAQPage Schema
How do I integrate scRNA-seq and ATAC data into joint embeddings for downstream analysis?▼

To integrate scRNA-seq and ATAC data into joint embeddings, you can use methods like CCA or WNN to align multiple single-cell modalities. Scribble handles preprocessing and batch correction to produce unified representations suitable for clustering and visualization.

What is the best way to combine RNA and protein data across multiple batches in single-cell analysis?▼

Combining RNA and protein data across batches in single-cell analysis requires multi-omics integration with batch correction. Scribble supports cross-modality alignment across samples, batches, and conditions to produce joint embeddings for downstream comparative analyses.

Can I use CCA and WNN integration methods for multi-omics single-cell data fusion?▼

Yes, you can use CCA and WNN integration methods for multi-omics single-cell data fusion. Scribble supports a range of integration strategies including CCA and WNN to combine RNA, ATAC, and protein data into unified joint embeddings.

Does the integration process handle preprocessing steps for single-cell modalities like RNA and ATAC?▼

Yes, the single-cell integration process handles preprocessing steps for RNA and ATAC modalities. Scribble manages preprocessing and integration to produce joint embeddings suitable for downstream analyses such as clustering and visualization.

When do I need multi-omics integration for single-cell sequencing data?▼

You need multi-omics integration for single-cell sequencing data when combining RNA, ATAC, and protein data across samples, batches, or conditions. Scribble produces unified joint embeddings to enable cross-modality alignment, data fusion, and comparative analyses across conditions.

Related Skills

Explore More Data & Analytics Skills→
Lord1EgyptLord1Egypt
2

scvi-tools

Run variational inference on annotated single-cell omics data matrices with scvi-tools.

Community
Advanced
chenyhvvvvchenyhvvvv
3

celltype-annotation-fast

Annotate cell types in spatial transcriptomics data using clustering, marker analysis, and LLM labeling.

Community
Intermediate
jackspacejackspace
16

scvi-tools

Model single-cell omics data with scvi-tools for batch-corrected analysis.

Community
Advanced
tony-zhelonkintony-zhelonkin
1

scglue-unpaired-multiomics-integration

Integrate unpaired scRNA-seq and scATAC-seq data using a guidance graph.

Community
Advanced