Geneviewer - Gene Cluster Visualizations in R

An R package that can be used to draw gene cluster arrow maps.

Shiny FASTA processor

A collection of Shiny applications to process FASTA sequence files.

Predicting Titanic passenger survival using tidymodels

In this post I explain how I build and tuned a Machine Learning model in R using the tidymodels package to predict passenger survival on the Titanic. I define some new features from the data to enhance the accuracy of the model and perform tuning of the model in Python using optuna. The final model reaches a top 2% score on Kaggle.

Tune R tidymodels with the Python optuna package

In this post I explain how I build and tuned a Machine Learning model in R using the tidymodels package. I then show how to tune the hyperparameters directly in R using a grid search and compare the results with performing the tuning in optuna using the reticulate package.

Optuna Samplers

An important step in building ML models is choosing a set of optimal hyperparameters. One of the best python packages to tune hyperparameters is Optuna. In this article I use Optuna to estimate the minimum and maximum of a simple function and try to illustrate, with a set of interactive graphs, what makes Optuna so efficient.

Shiny NGLVieweR - Interact with Protein Data Bank files in the web browser

I build a Shiny application that can be used to interact with Protein Data Bank (PDB) and structural files in the web browser. The application won a grand prices at the Shiny programming contest.

NGLVieweR - Interact with Protein Data Bank files in R and Shiny

I build an R package that can be used to interact with Protein Data Bank (PDB) and structural files in R and Shiny.

MS/MS Peptide Fragment Annotator

I build a Shiny application for the annotation of peptide fragment ions.

Rstudio Table Contest - winning entry

For the RStudio Table Contest I build an interactive employee directory using DT and R Shiny. The entry won 1st place.

Editable DataTables in R shiny using SQL

This tutorial describes how to make a DataTable in Shiny with Add, Edit, Copy and Delete functionality. Entries are stored in a local SQL database which makes it possible to retrieve the data between sessions.

Protein Fragment Finder

A small Shiny application that can match fragment masses that are detected by Mass Spectrometry to a protein sequence.