Spatial mapping of cell types by integration of transcriptomics data

Exploratory analysis of binary data in JAX

Code for the "Spatial genomics maps the structure, nature and evolution of cancer clones" paper

R toolkit for single cell genomics

A multi-view latent variable model with domain-informed structured sparsity for integrating noisy feature sets.

Computational method and analyses to study the clonality of circulating tumor cell clusters

Reference implementation of variational sequential Monte Carlo proposed by Naesseth et al. "Variational Sequential Monte Carlo" (2018)

LaTeX template for a PhD thesis at ETH Zurich

Estimation of clone-specific dynamical transition rate

Annotated data.

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

Spatiotemporal modeling of spatial transcriptomics

Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…

Single cell trajectory detection

Spatial Single Cell Analysis in Python

A declarative interactive genomics visualization library for Python.

A declarative library for Python designed to create interactive multi-scale visualizations of genomics and epigenomics data.

A novel machine learning pipeline to analyse spatial transcriptomics data

R pkg for Hierarchical Dirichlet Process

Football pitch plotting library for matplotlib

Tensorflow implementation of Hyperspherical Variational Auto-Encoders

LongSom tool for long-reads

Tree inference from mitochondrial mutations