Augusta: From RNA-Seq to gene regulatory networks and Boolean models.

ABSTRACT: Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of a GRN inferred from expression data is further refined by predicting transcription factor bindin

SUBMITTER: Musilova J 

PROVIDER: S-EPMC10837063 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature