CanSig Supplementary Information

This repository accompanies the CanSig tool and the preprint:

Josephine Yates, Florian Barkmann, Pawel Czyz, Agnieszka Kraft, Marc Glettig, Frederieke Lohmann, Elia Saquand, Richard von der Horst, Nicolas Volken, Niko Beerenwinkel and Valentina Boeva bioRxiv 2022.04.14.488324; doi: https://doi.org/10.1101/2022.04.14.488324

We store here our analyses, experiments, as well as the code to generate the figures, to increase reproducibility.

Contents

Benchmark

In benchmark/ directory we test the batch integration algorithms on a simulated dataset.

Dhaka implementation

In Dhaka-implementation/ directory we provide an unofficial PyTorch implementation of Dhaka dimension reduction method.

Notebooks

In notebooks/ directory we provide the notebooks that were used to generate the plots and the information for the experiments.