This page list software I have developed as part of my research work.
Assorted ImageJ scripts.
Automatization of small bioimage analysis tasks.https://github.com/hmbotelho/ImageJ-scripts
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.https://github.com/hmbotelho/fis_image_analysis
Exploring High Throughput Microscopy data with Shiny, Plotly and Fiji
An interactive web application based on the shiny R package, for high content data analysis. Enables data visualization (Fiji), quality control, plotting (Plotly) and statistical analysis (e.g. Z-score).https://github.com/embl-cba/shinyhtm
Systematic renaming of high throughput microscopy images
Handles imaging data from Leica and Zeiss microscopes.https://github.com/hmbotelho/htmrenamer
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.https://github.com/hmbotelho/convert_gene_compound_IDs
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.https://github.com/hmbotelho/CFTR_interactomes