Explore projects

Analyses of antimicrobial resistance genes in metagenomic data from patients with (multiple) recurrent Clostridioides difficile infections and their faecal microbiota transplantation donors - with culture data from multidrug resistant organisms

Engraftment calculations based on One Codex species-level taxonomic classifications of shotgun metagenomic read sets of the FECBUD trial - a collaboration between the Netherlands Donor Feces Bank and Vedanta Biosciences.

This repository gather all genomics data and analysis we performed on Zbtb24 in mouse embryonic stem cells.

RNA-seq pipeline for AML diagnostics. Illustration from Anatomy & Physiology, licenced under the Creative Commons Attribution 3.0 Unported

Code used to prepare disease data in survival format, calculate LRC score, data QC and preparation, and data analyses.

Functional metagenomics analysis using the HUMAnN tool version 3

Microbiota analyses of metagenomic samples of ulcerative colitis patients and fecal microbiota transplantation donors in the FECBUD trial

Project NGS code with Van der Weegen et al; ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation; NCB 2021

miRNA mRNA Expression Integration

Mobile student exchange program

R library for simulating digital PCR experiments.

Leiden450K contains a couple of functions for preprocessing of Illumina Human 450K array data, such as reading idat files in parallel, filtering probes and normalization.

Scripts used for differential gene expression analysis and its reporting (currently for RNA-seq data)