Gerstung Lab

PC-CHiP

Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis

MutationTimeR

An R package to time somatic mutations

SARS-CoV-2-International

International SARS-CoV-2 surveillance

BaSISS

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

PCAWG-11

Code accompanying "The evolutionary history of 2,658 cancers", Nature 578, 122–128 (2020)

deepSNV

The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.

tensorsignatures

A python package for learning mutational signatures and their multidimensional genomic properties

Delphi

sarscov2-b117

Spatiotemporal analysis of strain-specific B.1.1.7 SARS-CoV-2 infection dynamics

genomicsurveillance

CancerRisk

CoxHD

An R package containing high-dimensional extensions of the Cox model

signature-interactions

Mutational signatures are jointly shaped by DNA damage and repair

BarrettsProgressionRisk

An R package to process and predict risk of adenocarcinoma progression from shallow whole-genome sequencing data.

postcode

Decoding of image-based spatial transcriptomics

CHOCOLAT-G2P

ebmstate

An R package for Empirical Bayes MultiState models

ebmstate_paper_data_files

ebsurv

mutationaccumulation

Codes for a publication about mutation accumulation in >60 DNA repair deficient C. elegant lines (Meier et al, under preparation).

SARS-CoV-2-Germany

SARS-CoV-2 genomic surveillance in Germany

scHierarchy

A toolking for cell type hierarchies: marker selection & consistent classification

omero_setup

clonal_dynamics

Code repository for the longitudinal and phylodynamic analysis in "The longitudinal dynamics and natural history of clonal haematopoiesis"

gerstung-lab.github.io

ProbCox

Probabilistic Cox Regression

radiation

Codes for the analysis of C. elegant samples of different DNA repair deficient backgrounds exposed to ionising radiation.

segger

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

uk_biobank_survival

wbs-prediction

Code repository for a project focused on diagnostic prediction from whole blood slides