Plate IV.56 · Publications
Protocol for Predicting Cell Fate Responses to in Silico Perturbation using RegVelo, from Code to Agentic Platform Analysis
Preprint in SSRN, 2026.
Abstract
Here, we present a regulatory velocity (RegVelo) analysis pipeline for inference of gene-regulatory coupled transcriptome-wide splicing dynamics and in silico transcription factor perturbation. We describe four key computational steps including scRNA-seq preprocessing and integration with gene regulatory network, model training, cell fate prediction and TF perturbation. Additionally, we demonstrate chat-based usage of the analysis pipeline with Biomni lab agentic workflow. For complete details on the use and execution of this protocol, please refer to Wang et al. 2026.
Cite
@misc{ryhanen2026protocol,
title = {{Protocol for Predicting Cell Fate Responses to in Silico Perturbation using RegVelo, from Code to Agentic Platform Analysis}},
author = {Ryhänen, Emma Aino Elina and Wang, Weixu and Zhang, Serena and Tachibana, Kikue and Theis, Fabian J.},
howpublished = {SSRN},
publisher = {Elsevier BV},
year = {2026},
doi = {10.2139/ssrn.7447814},
url = {https://doi.org/10.2139/ssrn.7447814},
note = {Preprint}
}