arboreto
Category: life-sciences · License: BSD-3-Clause license · Version: 1.1 · Includes scripts
Tags: gene regulatory networks, GRNBoost2, transcriptomics, single-cell, bioinformatics
When to use it
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.Example requests
Ask your agent in plain language, for example:- “How do I infer a TF-target network from my expression matrix with GRNBoost2?”
- “I have a 12,000-cell scRNA-seq dataset in pbmc.h5ad and a list of human TFs in allTFs_hg38.txt. I ran grnboost2 in a script on Windows and got a Dask error: ‘An attempt has been made to start a new process before the current process has finished its bootstrapping phase.’ How do I fix this and run it properly?”
- “I want to figure out which transcription factors are likely driving gene expression changes across my 200 bulk liver samples. I’d like a ranked list of regulator-to-target gene links I can then feed into a downstream regulon analysis. What should I do?”
Install
/plugin marketplace add KalarisLabs/research-agent-skills and install the whole life-sciences category with /plugin install life-sciences@research-agent-skills.