Agent skill · research science · aiskillstore
arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
Why this skill is useful
Provides specific algorithms and methods for inferring gene regulatory networks from transcriptomics data that the AI wouldn't reliably generate on its own.
What it needs
Requires arboreto installed locally. About 4k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
Arboreto Overview Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using parallelized algorithms that scale from single machines to multi-node clusters. Core capability: Identify which transcription factors (TFs) regulate which target genes based on expression patterns across observations (cells, samples, conditions). Quick Start Install arboreto: Basic GRN inference: Critical: Always use if name == 'main': guard because Dask spawns new processes. Core Capabilities 1. Basic GRN Inference For standard GRN inference workflows including: Input data preparation (Pandas DataFrame or NumPy array) Running inference with GRNBoost2 or GENIE3 Filtering by transcription factors Output format and interpretation See: references/basicinference.md Use the ready-to-run script: scripts/basicgrninference.py for standard inference tasks: 2. Algorithm Selection Arboreto provides two algorithms: GRNBoost2 (Recommended): Fast gradient boosting-based inference Optimized for large datasets (10k+ observations) Default choice for most analyses GENIE3: Random Forest-based inference Original multiple regression approach Use for comparison or validation Quick comparison: For detailed algorithm comparison, parameters, and selection guidance: references/algorithms.md 3. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/arboreto--b77198