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.


Team

Xiaoqing Guan downloaded and processed the datasets, implemented the analysis scripts, developed applications, and wrote the documents.

The web server was developed by Meng Cai and Yang Du.

The project was designed and supervised by Dr. Jianmin Wu


Acknowledgements

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 Analysis.
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 Implementation.
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 S.
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): p. 15545-50.
Software version 3.0. https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/3.0/