Causal and Experiment Analysis

MISO: An open-source LIMS for NGS sequencing centres

The code for the paper "Modelling the Aqueous Transport of an Infectious Pathogen in Regional Communities: Application to the Cholera Outbreak in Haiti"

papaja (Preparing APA Journal Articles) is an R package that provides document formats to produce complete APA manuscripts from RMarkdown-files (PDF and Word documents) and helper functions that fa…

Input files and scripts related to our study entitled "Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020" (Bollen et al. 2021…

Course repository for Columbia University's EEEB UN3005/GR5005 (spring 2020)

Code, data, and figures for a study of rodent interactions within the Lassa virus system

This repository contains code for a pathogen forecasting framework. Here, the framework is applied to Lassa virus, the causative agent of Lassa fever in humans.

Stable clustering of SARS-CoV-2 sequences from phylogenetic trees

Bioinformatics Pipeline and Visualization resources

R code to produce Demographic and Health Survey Indicators

A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via metadata templ…

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by …

A GLUE project for comparative genomic analysis of flaviviruses

Amplicon Sequencing Analysis Pipeline

NGS-1 Data analysis course

Evolutionary analysis of USVI Zika epidemic

Pathogen evolution, selection and immunity

Online material for the Perspective: "Julia for Biologists" presented at JuliaCon 2021: https://www.youtube.com/watch?v=gRj7E5kYG1I

GPT4 & LangChain Chatbot for large PDF docs

A minimal & modern LaTeX template for your (bachelor's | master's | doctoral) thesis

Spit shine for Jupyter notebooks 🧽✨

Examples of analyzing microbiome data in Goolge Colab

Scripts to run results in PNAS

Source code and related materials for the O'Reilly book