arboreto

What problem does it solve?

This Skill automates the inference of gene regulatory networks (GRNs) from gene expression data, helping researchers understand complex biological systems.

Core Features & Use Cases

• GRN Inference: Identifies transcription factor-target gene relationships using scalable algorithms like GRNBoost2 and GENIE3.
• Data Analysis: Suitable for transcriptomics data (RNA-seq) to uncover regulatory interactions.
• Distributed Computing: Supports scaling analysis to large datasets using Dask.
• Use Case: Analyze single-cell RNA-seq data to discover key regulatory pathways driving cell differentiation.

Quick Start

Use the arboreto skill to infer a gene regulatory network from the provided expression data file named 'expression_data.tsv' and save the output to 'network.tsv'.