CVCDAP stands for Cancer Virtual Cohort Discovery Analysis Platform. It can help perform cohort-level rapid and effective re-discovery of integrated mulit-omics data for your research questions. This website is free and open to all users.
Xiaoqing Guan downloaded and processed the datasets, implemented the analysis scripts, developed applications, and wrote the documents.
The project was designed and supervised by Dr. Jianmin Wu.
The genomic datasets were from https://gdc.cancer.gov/about-data/publications/pancanatlas
The proteomic datasets were from CPTAC.
The following R packages and softwares are used in CVCDAP analysis.
|Alboukadel Kassambara and Marcin Kosinski (2019). survminer: Drawing Survival Curves using 'ggplot2'. R package version 0.4.4. https://CRAN.R-project.org/package=survminer|
|Kevin Blighe (2019). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. R package version 1.0.1. https://github.com/kevinblighe/EnhancedVolcano|
|Raivo Kolde (2019). pheatmap: Pretty Heatmaps. R package version 1.0.12. https://CRAN.R-project.org/package=pheatmap|
|Mayakonda, A., et al., Maftools: efficient and
comprehensive analysis of somatic variants in cancer. Genome
Res, 2018. 28(11): p. 1747-1756.
R package version 1.8.0. https://bioconductor.org/packages/release/bioc/html/maftools.html
|H. Wickham (2016). ggplot2: Elegant Graphics for Data
R package version 3.1.1. https://cran.r-project.org/web/packages/ggplot2
|Rachel Rosenthal (2016). Rosenthal, R., et al.,
deconstructSigs: delineating mutational processes in single
tumors distinguishes DNA repair deficiencies and patterns of
carcinoma evolution. Genome Biology, 2016. 17(1): p. 31.
R package version 1.8.0. https://CRAN.R-project.org/package=deconstructSigs
|Jesse H. Krijthe (2015). Rtsne: T-Distributed
Stochastic Neighbor Embedding using a Barnes-Hut
R package version 0.15. https://github.com/jkrijthe/Rtsne
|Ritchie, M.E., et al., limma powers differential
expression analyses for RNA-sequencing and microarray studies.
Nucleic Acids Res, 2015. 43(7): p. e47.
R package version 3.38.3. https://bioconductor.org/packages/release/bioc/html/limma.html
|Therneau T (2015). A Package for Survival Analysis in
R package version 2.43.3. https://CRAN.R-project.org/package=survival
|Vincent Q. Vu (2011). ggbiplot: A ggplot2 based biplot.
R package version 0.55. http://github.com/vqv/ggbiplot
|Subramanian, A., et al., Gene set enrichment analysis:
a knowledge-based approach for interpreting genome-wide
expression profiles. Proc Natl Acad Sci U S A, 2005. 102(43):
Software version 3.0. https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/3.0/