Prostate Cancer Alteration Signature Analysis Report

tool sigminer: https://shixiangwang.github.io/sigminer-doc/
manuscript: Wang S, Li H, Song M, Tao Z, Wu T, He Z, et al. (2021) Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genet 17(5): e1009557. https://doi.org/10.1371/journal.pgen.1009557

The both methods ("Wang" and "Macintyre") are available at Sigminer v1.2.5 (https://cran.r-project.org/src/contrib/Archive/sigminer/).

For reproducing the Cox result shown in manuscript, please refer to this script.

LICENSE

Cancer Biology Group @ShanghaiTech

Research group led by Xue-Song Liu in ShanghaiTech University

Name		Name	Last commit message	Last commit date
Latest commit History 173 Commits
.vscode/vscode-R		.vscode/vscode-R
additional-analysis		additional-analysis
analysis		analysis
check		check
cnv_calling		cnv_calling
data		data
dbGap		dbGap
dirtycode		dirtycode
docs		docs
figures		figures
figures_new		figures_new
output		output
.gitignore		.gitignore
Macintyre_single_sample_fitting_test.md		Macintyre_single_sample_fitting_test.md
README.md		README.md
paper_figures.R		paper_figures.R
prad_signature.Rproj		prad_signature.Rproj
supp_plus_analysis.R		supp_plus_analysis.R
supp_tables.R		supp_tables.R
survival-analysis-check-and-update.R		survival-analysis-check-and-update.R
table_S6.xlsx		table_S6.xlsx
table_S7.xlsx		table_S7.xlsx
tcga_prad.rds		tcga_prad.rds
update_site..R		update_site..R