alterlab-arboreto
CommunityInfer gene regulatory networks from expression data.
Data & Analytics#arboreto#gene-regulatory-network#distributed-computing#single-cell-rna-seq#grnboost2#genie3#bulk-rna-seq
AuthorAlterLab-IEU
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Arboreto enables scalable inference of gene regulatory networks (GRNs) from gene expression data using parallelized algorithms (GRNBoost2, GENIE3) to identify regulatory relationships between transcription factors and target genes.
Core Features & Use Cases
- Scale: supports large datasets from bulk and single-cell RNA-seq
- Algorithms: GRNBoost2 (recommended) and GENIE3 for validation
- Distributed compute: leverages Dask for local or cluster execution
- Output: returns TF–target–importance triplets suitable for downstream analyses
Quick Start
Install Arboreto and run GRN inference on your expression matrix to generate a regulatory network.
Dependency Matrix
Required Modules
pandasarboreto
Components
scriptsreferences
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Please help me install this Skill: Name: alterlab-arboreto Download link: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/archive/main.zip#alterlab-arboreto Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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