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aml-multistage

Code accompanying Precision oncology for acute myeloid leukemia using a knowledge bank approach

barrettsprogressionrisk

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

basiss

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

cancerrisk

chocolat-g2p

clonal_dynamics

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

clonex

Efficient Wright-Fisher simulations for intra-tumour population genetics

coxhd

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

deepsnv

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

delphi

ebmstate

An R package for Empirical Bayes MultiState models

ebmstate_paper_data_files

ebsurv

genomicsurveillance

gerstung-lab.github.io

mds-expression

R code for Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes

mmr

C. elegans and ICGC cancer data analysis for (Meier, Volkova et al. 2017)[https://www.biorxiv.org/content/biorxiv/early/2017/06/13/149153.full.pdf].

mpn-multistage

MPN multistage calculator

mutationaccumulation

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

mutationtimer

An R package to time somatic mutations

omero_setup

pc-chip

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

pcawg-11

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

postcode

Decoding of image-based spatial transcriptomics

preaml

Code accompanying Prediction of AML risk in healthy individuals by Abelson, Collord, et al. (2018), Nature, 559:400-404

probcox

Probabilistic Cox Regression

radiation

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

sars-cov-2-germany

SARS-CoV-2 genomic surveillance in Germany

sars-cov-2-international

International SARS-CoV-2 surveillance

sarscov2-b117

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