Shon Kurian George

Spatial Transcriptomics Pipeline Development
Image-based cell profiling (cypro : R package)

Edinburgh, United Kingdom & Kerala, India · Reachable on Email/LinkedIn · Open to Collaboration

About

Bioinformatician with an MSc in Bioinformatics from the University of Edinburgh shipping reproducible analyses and tools with an interest in providing interactive, easy-to-use applications. Skilled in R, Python, Bash Scripting and building bioinformatic pipelines.

Skills

  • R / Shiny, Python, bash scripting
  • Spatial transcriptomics (SPATA2, Seurat)
  • Git/GitHub, Docker, AWS EC2, Nextflow
  • Vim, Ollama, Open WebUI, Claude, ChatGPT

Work Experience

cypro R Package

R Package Developer · Nov 2024 – Present

Developing an R package to streamline image-based cell profiling workflows by integrating data from diverse platforms including CellProfiler and CellTracker. Enhanced package usability by implementing intuitive Shiny-based interfaces that allow detailed specification down to individual well-level configurations, significantly simplifying user interaction.

Refined S4 class objects within cypro to ensure accurate data integration from imaging platforms, enabling comprehensive cell movement analyses. Incorporated proactive user warnings and notifications within the Shiny application, minimising user errors, safeguarding data integrity, and enhancing the overall user experience.

View GitHub repo

10x Visium Spatial Transcriptomics Pipeline to Analyse miRNA Expression Patterns

MSc Bioinformatics Dissertation · Mar 2024 - Sep 2024

Developed an end-to-end pipeline to investigate whether miRNAs act as guardians of gene expression at cell-type boundaries. Utilised SPATA2 and Seurat frameworks to process datasets into analysis-ready form, then performed BayesSpace and Hartigan-Wong K-means clustering to segregate cell types.

Conducted TargetScan miRNA target analysis across 8 datasets (brain, heart, liver), detecting tissue-specific miR-124 (brain) and miR-1 (heart) with high confidence. Identified neighbouring clusters showing high and low target expression for both miRNAs. Built an accompanying Shiny app to interactively view the analysis results (SPATA2 Shiny App).

View GitHub repo

Interactive Applications (Hosted on AWS EC2)

Projects