CCB, NKI

Notebooks to reproduce the figures from CNR manuscript (Bosdriesz et al., 2018 https://doi.org/10.1101/243709)

Flexible gene set enrichment analysis

A method for network reconstruction and quantification from perturbation experiments

Infers a topology of relationships between different datasets, such as multi-omics and phenotypic data recorded on the same samples.

Multivariate probability density approximation R package

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

A non-linear mixed effects model for estimating compound sensitivity

An R Markdown file containing code to reproduce all figures from our iTOP publication

A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream featu…

The Multitask Variable Importance (Multitask VI) is a modified version of the permuted variable importance score for Random Forests. Essentially, for a Random Forest trained simultaneously for multiple response vectors, it allows the inference of variable importance scores per variable and per task.

Tool for identifying transposon insertions and their effects from RNA-seq data.

Functional Sparse-Factor Analysis

RUBIC detects recurrent copy number aberrations.

Common Insertion Site Mapping Platform implemented as an R package for statistical analysis of retroviral insertional mutagenesis screens.

R package for the Detection of Imbalanced Differential Signal (DIDS) algorithm.

R code for Kernel Convolved Rule Based Mapping