Software Summary

This page list software I have developed as part of my research work.

Bioimage analysis

  • Quantification of Forskolin Induced Swelling (FIS) imaging data

    Pipelines for the quantification of time-dependent organoid cross-sectional area changes using CellProfiler or ImageJ.

    The FIS assay is a high-content screening assay designed for personalized medicine approaches in Cystic Fibrosis using intestinal organoids. The ImageJ scripts include a custom algorithm for object tracking and hole filling. Read the original publication here.

High content analysis

R packages


  • Conversion of compound and gene names

    R scripts which convert between synonym identifiers of compounds (e.g. CAS, ChEMBL, ZINC) and genes (e.g. gene symbol, Uniprot ID, Ensembl gene).

    Data is collected from online databases using the biomaRt and Rentrez R packages, or API access.
  • Gene heatmap

    Simple hierarchical clustering of gene expression data.

    Interactive web application based on the R shiny package. Avaliable online here.
  • CFTR interactomes

    A tidy selection of published CFTR interactomes (or CFTR-related omics datasets).

    Data is collected directly from the original publications. Gene names have been harmonized across datasets to allow direct comparison.