Software

Open-source tools and reproducible workflows that I have developed or contributed to, with a focus on alternative splicing analysis, microexon discovery, and RNA regulatory genomics.

MicroExonator

MicroExonator is a Snakemake-based workflow for the de novo discovery and quantification of microexons from RNA-seq data. It was designed to address a common limitation of standard RNA-seq pipelines: very short exons are often missed by general-purpose splicing workflows. MicroExonator enables systematic microexon discovery and PSI quantification across bulk and selected full-length or total-RNA single-cell RNA-seq datasets.

Keywords: Snakemake, RNA-seq, microexons, alternative splicing, PSI, reproducible workflows.

GitHub repository Genome Biology, 2021 Methods chapter (2022)

Workflow and analysis identity

Beyond MicroExonator, my work uses reproducible workflow management, large-scale RNA-seq processing, and machine learning to study RNA regulation across tissues, cell types, and disease cohorts. I develop and maintain Snakemake pipelines that combine splicing quantification with sequence-based machine-learning models, integrated with family-based genetics for variant interpretation in neurodevelopmental disorders.

Technical skills

Python
R
Unix / shell
Snakemake
Git
Conda
HPC
GPU computing
PyTorch / JAX
Bulk RNA-seq
Single-cell RNA-seq
Total-RNA sequencing
Alternative splicing analysis
Microexon discovery
PSI quantification
Sequence-based splicing models
Variant effect prediction
Rare-variant / family-based genetics

GitHub profile

All code is hosted under open-source licences.
github.com/geparada