arboreto SKILL.md skillA
arboreto from aicodedecode/awesome-muse-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add aicodedecode/awesome-muse-skills/arboreto@git:20260927.806f3e1Pins git:20260927.806f3e1 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- aicodedecode/awesome-muse-skills
- Path
skills-imported/arboreto/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260927.806f3e1, committed Sep 27, 2026
- Size
- 6,857 bytes
- Repository stars
- 25
- License
- MIT
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# 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:
```bash
uv pip install arboreto
```
Basic GRN inference:
```python
import pandas as pd
from arboreto.algo import grnboost2
if __name__ == '__main__':
# Load expression data (genes as columns)
expression_matrix = pd.read_csv('expression_data.tsv', sep='\t')
# Infer regulatory network
network = grnboost2(expression_data=expression_matrix)
# Save results (TF, target, importance)
network.to_csv('network.tsv', sep='\t', index=False, header=False)
```
**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)
…Read the whole file at its exact version.
How to install
mdr add aicodedecode/awesome-muse-skills/arboreto@sha256:5723a054405c0506The line at the top of this page pins the label git:20260927.806f3e1, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_qourn35h4pjlrqu7)
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Versions
The registry has recorded 1 version of this file, committed on Sep 27, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (6857 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
aicodedecode/awesome-muse-skills · 25 stars · license MIT · pushed 2026-10-10 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_qourn35h4pjlrqu7 GET https://markdownregistry.com/api/v1/resolve?ref=aicodedecode/awesome-muse-skills/arboreto GET https://markdownregistry.com/api/v1/blob/5723a054405c0506581a0b27490b7316eb0c35312568373e95ac7779d368abf1
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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