ShixiangWang / absoluteCNVdata

Pre-compiled absolute CNV data, which can be used for package sigminer/VSHunter and CNV analysis

absoluteCNVdata

Pre-compiled absolute CNV data, which can be used for package sigminer (examples or data mining) and related CNV analysis.

.rda and .RData file can read with load() function, .rds file can read with readRDS() function.

TCGA pancan ABSOLUTE calling results

Generate from Synapse, paper link https://www.nature.com/articles/nbt.2203

• pancan12_absolute.rda
• pancan12_info.rda

CNV signature results from BriTROC-1 study

Generate from https://www.nature.com/articles/s41588-018-0179-8

• example_cn_QDNASeq.RData
• component_parameters.rds
• NatGen_features.rda

Chromosome size of hg19 and hg38

• hg19.chrom.sizes.txt
• hg38.chrom.sizes.txt

Citation

Wang, Shixiang, et al. "APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer." Oncogene (2018).

Reference

• Carter, S. L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T., ... & Beroukhim, R. (2012). Absolute quantification of somatic DNA alterations in human cancer. Nature biotechnology, 30(5), 413.
• Macintyre, G., Goranova, T. E., De Silva, D., Ennis, D., Piskorz, A. M., Eldridge, M., ... & Dowson, S. (2018). Copy number signatures and mutational processes in ovarian carcinoma. Nature genetics, 50(9), 1262-1270.