CCB, NKI

DISCOVER

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

flexgsea-r

Flexible gene set enrichment analysis

PRECISE

sobolev_alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

TRANSACT_manuscript

Scripts supporting TRANSACT manuscript

imagene-analysis

Radiogenomic analysis of breast cancer by linking MRI phenotypes with tumor gene expression

imfusion

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

MixedIC50

A non-linear mixed effects model for estimating compound sensitivity

TANDEM

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 features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.

RUBIC

RUBIC detects recurrent copy number aberrations.

multitask_vi

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.

TRANSACT

Python implementation of TRANSACT, a tool to transfer non-linear predictors of drug response from model systems to tumors.

cimpl

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

funcsfa

Functional Sparse-Factor Analysis

iTOP

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

Percolate

Implementation of Percolate, an exponential family JIVE statistical model for multi-view integration

ppbc

Post-partum breast cancer

won-parafac

Weighted orthogonal non-negative (WON) parallel factor analsyis (PARAFAC)

cnr

A method for network reconstruction and quantification from perturbation experiments

Percolate_manuscript

sobolev_alignment_manuscript

Tumor-educated-platelets

Code accompanying the publication "Tumor educated platelets for breast cancer detection"

bcm3

BCM3 - Bayesian Inference for Computational Models

CNR-analyses

Notebooks to reproduce the figures from CNR manuscript (Bosdriesz et al., Bioinformatics, 2018)

iTOP-RMarkdown

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

mvdens

Multivariate probability density approximation R package

PRECISE_figures

Jupyter notebooks and code to reproduce figures

precision-immune-analyses

Analyses for the PRECISION DCIS immune paper (in press)

prepost_neoadjuvant

scMeMo-paper