Welcome to the complementary web portal for our study characterizing chromosomal instability using copy number signatures.

Drews et al., Nature (2022)

Here you will find a collection of links to supporting material outside the main manuscript, as well as the opportunity to explore the signatures, their definitions, activities across the TCGA cohort and their association with common covariates.

Contact for collaboration

Please contact Florian Markowetz and Geoff Macintyre

Supplementary information

• Supplementary materials

Code repositories

• Drews2022_CIN_Compendium is the main GitHub repository containing code to reproduce the figures, most results and most supplementary tables
• CINSignatureQuantification covers the R package needed to quantify signature activities from copy number profiles. Also includes clinical classifier
• CINSignatureDiscovery covers (1) how the signature compendium was obtained and (2) details how to identify de-novo signatures from copy number profiles
• CINSignatureGenomeSimulation covers the simulation we used to validate the multi-feature approach
• CINSignatureBiomarkerAnalysis supports the results shown in Figure 3
• CINSignatureInterpretationMatrix details how the Interpretation matrix was obtained
• CINSignatureInterpretationAnalysis supports all analyses performed using the Interpretation matrix
• CINSignatureCellLines details how the raw cell line data was processed to be used for the analyses covered in Figure 3
• CINSignatureSWGSBinSize details how the bin size was calculated that has been used to downsample the WGS to shallow WGS data
• ASCAT is the tool used to generate absolute copy number profiles from Affymetrix SNP6 arrays. The final copy number profiles can be downloaded from the github repository