"A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels"

https://doi.org/10.1038/s41388-020-1367-4 Lundberg et al.

Written by ARIAN LUNDBERG

All R codes (R statistical software version 3.5.3) to reproduce main and supplemental figures of "A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels" Lundberg et al. are available in "~/Codes/"

The following RData files were used in the codes.

PANCAN.RData

is an ExpressionSet created by using public data available at the following link and/or publications:
https://gdc.cancer.gov/about-data/publications/pancanatlas

RNA expression data

RNA (Final) - EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv

Clinical with Follow-up

Clinical with Follow-up - clinical_PANCAN_patient_with_followup.tsv Additional patients survival information downloaded from ref 19. Liu et al.

iCluster and Aneuploidy data:

downloaded from ref 17. Hoadley et al.

CCS.genes.RData:

a list of genes used to make the Cell cycle score (CCS) in the original publication. ref 11. Lundberg et al.

Cancer.abb.RData:

RData generated to assign colors to different cancer types used in the main and supplemental figures of this publication.

Support or Contact

Please contact Arian Lundberg : [email protected] if you have any furthur questions.

Sincerely, Arian Lundberg