regulAS: A Bioinformatics Tool for the Integrative Analysis of
  Alternative Splicing Regulome using RNA-Seq data
Sofya Lipnitskaya
The regulAS software package is a bioinformatics tool designed to support
computational biology researchers in investigating regulatory mechanisms of
splicing alterations through integrative analysis of large-scale RNA-Seq data
from cancer and healthy human donors, characterized by TCGA and GTEx projects.
This technical report provides a comprehensive overview of regulAS, focusing on
its core functionality, basic modules, experiment configuration, further
extensibility and customisation.
  The core functionality of regulAS enables the automation of computational
experiments, efficient results storage and processing, and streamlined workflow
management. Integrated basic modules extend regulAS with features such as
RNA-Seq data retrieval from the public multi-omics UCSC Xena data repository,
predictive modeling and feature ranking capabilities using the scikit-learn
package, and flexible reporting generation for analysing gene expression
profiles and relevant modulations of alternative splicing aberrations across
tissues and cancer types. Experiment configuration is handled through YAML
files with the Hydra and OmegaConf libraries, offering a user-friendly
approach. Additionally, regulAS allows for the development and integration of
custom modules to handle specialized tasks.
  In conclusion, regulAS provides an automated solution for alternative
splicing and cancer biology studies, enhancing efficiency, reproducibility, and
customization of experimental design, while the extensibility of the pipeline
enables researchers to further tailor the software package to their specific
needs. Source code is available under the MIT license at
https://github.com/slipnitskaya/regulAS.