How does this integrate with the SCENIC pipeline?

Arboreto is a core component of the pySCENIC workflow, handling the initial step of inferring the potential regulatory links between genes.

Can Arboreto handle single-cell RNA-seq data?

Yes, Arboreto is highly optimized for large-scale transcriptomics, making it an ideal choice for the high cell counts found in single-cell RNA-seq datasets.

Do I need a computing cluster to use this skill?

No. While Arboreto supports distributed computing via Dask for multi-node clusters, it works efficiently on local multi-core machines automatically.

What algorithms does Arboreto support for GRN inference?

Arboreto primarily supports GRNBoost2 (a fast gradient boosting-based approach) and GENIE3 (the classic Random Forest-based approach).

Arboreto GRN Inference

Name: Arboreto GRN Inference
Author: jimmc414

byjimmc414

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324

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数据科学与机器学习

Infers gene regulatory networks from transcriptomics data using scalable algorithms like GRNBoost2 and GENIE3.

Arboreto is a specialized computational tool integrated with Claude Code for bioinformaticians and researchers to map transcription factor-target gene interactions. It enables the reconstruction of complex gene regulatory networks (GRNs) from large-scale bulk or single-cell RNA-seq datasets using high-performance algorithms. By leveraging distributed computing via Dask, Arboreto facilitates autonomous biological discovery, allowing users to identify key regulatory drivers and interpret gene expression patterns across diverse experimental conditions.

主要功能

01Transcription factor filtering for targeted regulatory mapping

02324 GitHub stars

03Support for large-scale bulk and single-cell RNA-seq datasets

04Scalable GRN inference using GRNBoost2 and GENIE3 algorithms

05Automated scripts for standard genomic analysis workflows

06Distributed computing integration with Dask for cluster scaling

使用场景

01Integrating GRN inference as a core component of the pySCENIC pipeline

02Reconstructing regulatory networks for disease vs. control comparative analysis

03Identifying transcription factor-target gene relationships in single-cell datasets

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos arboreto

For use in Claude.ai and ChatGPT

Download Skill