AN
数据与复现
AnnData
AnnData is a Python package for handling annotated data matrices, storing experimental measurements (X) alongside observ…
K-Dense-AI/claude-scientific-skills查看
数据与复现
AR
Arboreto
维护者 K-Dense Inc. · 最近更新 2026年4月1日
Arboreto is a computational library for inferring gene regulatory networks (GRNs) from gene expression data using paralleli.
原始来源
K-Dense-AI/claude-scientific-skills
https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/arboreto
- 维护者
- K-Dense Inc.
- 许可
- BSD-3-Clause license
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- Arboreto是一个computational 库 ，用于 inferring gene regulatory networks (GRNs) ，面向 gene expression data ，使用 parallelized algorithms that scale ，面向 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)。
- network_grnboost = grnboost2(expression_data=matrix)。
原始文档
SKILL.md 摘录
Quick Start
Install arboreto:
Basic GRN inference:
Critical: Always use if __name__ == '__main__': guard because Dask spawns new processes.
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/basic_inference.md
Use the ready-to-run script: scripts/basic_grn_inference.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:
from arboreto.algo import grnboost2, genie3
适用场景
- 适合在analyzing transcriptomics data (bulk RNA-seq，single-cell RNA-seq) to identify transcription factor-target gene relationships 、 regulatory interactions时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
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