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analysis-geniml

Official

ML for genomic intervals

Data & Analytics#embeddings#machine learning#bioinformatics#genomics#scATAC-seq#bed files
Authorbiomaps-infra
Version1.0.0
Installs0

System Documentation

What problem does it solve?

This Skill streamlines machine learning tasks involving genomic interval data (like BED files), automating complex analyses that would otherwise require extensive custom scripting and bioinformatics expertise.

Core Features & Use Cases

  • Genomic Embeddings: Train Region2Vec or BEDspace models to represent genomic regions and their associated metadata in a low-dimensional space.
  • Single-Cell Analysis: Utilize scEmbed for clustering and analyzing single-cell ATAC-seq data.
  • Reference Building: Construct consensus peak sets (universes) for standardized genomic analysis.
  • Use Case: Analyze scATAC-seq data to identify distinct cell populations by training an scEmbed model and then using scanpy for clustering and visualization.

Quick Start

Use the analysis-geniml skill to train Region2Vec embeddings on BED files located in the 'bed_files/' directory, saving the model to 'model/'.

Dependency Matrix

Required Modules

None required

Components

references

💻 Claude Code Installation

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Please help me install this Skill:
Name: analysis-geniml
Download link: https://github.com/biomaps-infra/blender-opencode/archive/main.zip#analysis-geniml

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