Explore projects

Some old code for visualizing mtDNA SNPs

This repo contains source code for the paper "Controlling bias and inflation in epigenome- and transcriptomewide association studies using the empirical null distribution" by Maarten van Iterson, Erik W. van Zwet and Bastiaan T. Heijmans.

Short presentation on PyVCF

Comparative genomics project of Ruminococcus gnavus, with additional prevalence and abundance analysis of worldwide metagenomic datasets.

Mirror of https://github.com/LUMC/mutalyzer.git

R scripts that could be useful for analysis in RP3. For example, extracting information from the metaDb, calculating GC content and length based on the exons files, RNAseq normalization e.g. cqn, ...

Presentations and posters on Mutalyzer

Public repository containing the code for the open source WebGL viewer based on BabylonJS

Functional metagenomics analysis using the HUMAnN tool version 3

Interactive Volcano Plots

Mutalyzer DNA Visualisation

This pipeline takes paired-end fastq files, does a quick genome assembly on them (via Velvet + kmergenie), and predicts antibiotic resistance via abricate.

Mirror of Open Grid Engine code -- with modifications

NGS LIMS

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