At Molepi we develop statistical and bioinformatical methodology necessary for the analysis of data generated by novel–omics technologies. Below is a brief overview of the software that has been developed within our department.
DNAmArray : Streamlined workflow for the quality control, normalization and bias-free analysis of Illumina methylation array data - The Leiden approach.
MethylAid : A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.
Bacon : Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.