Resources

Our software and datasets

Bioconductor packages and other software

This package provides functionality for performing divergence analysis as presented in Dinalankara et al, “Digitizing omics profiles by divergence from a baseline”, PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features. Here you can download the R Bioconductor package divergence

The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle). Here you can download the R Bioconductor package switchBox

The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance. The package contains utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis. Here you can download the R Bioconductor package matchBox

The RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms, experiments, studies, and more. Here you can download the R Bioconductor package RTopper

The package contains gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test. specifically, the package contains RGList objects from the Glas and Buyse breast cancer studies. Here you can download the R Bioconductor package mammaPrintData

Gene expression data for the two breast cancer cohorts published by van’t Veer and Van de Vijver in 2002. The data is distributed in the form of ExpressionSets from these two cohorts (van’t Veer and Van de Vijver breast cancer studies). Here you can download the R Bioconductor package seventyGeneData