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

• ImageJ scripts

  Assorted ImageJ scripts.

  Automatization of small bioimage analysis tasks.

  https://github.com/hmbotelho/ImageJ-scripts

• 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.

  https://github.com/hmbotelho/fis_image_analysis

• shinyHTM

  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
• Organoid Analyst

  Statistical analysis of the Forskolin-Induced Swelling (FIS) assay

  Interactive web application based on the shiny R package. Read the original publication here.

  https://github.com/hmbotelho/organoid_analyst
• Sample data

  Sample data for high-throughput microscopy image and data analysis.

  https://github.com/hmbotelho/sample_data https://github.com/hmbotelho/sample_data

• htmrenamer

  Systematic renaming of high throughput microscopy images

  Handles imaging data from Leica and Zeiss microscopes.

  https://github.com/hmbotelho/htmrenamer

• 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.

  https://github.com/hmbotelho/convert_gene_compound_IDs
• Gene heatmap

  Simple hierarchical clustering of gene expression data.

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

  https://github.com/hmbotelho/gene_heatmap
• 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.

  https://github.com/hmbotelho/CFTR_interactomes