References for the R package used by CBioExplorer
| R Package | Version | Citation |
|---|---|---|
| table1 | 1.2 | Benjamin Rich (2020). table1: Tables of Descriptive Statistics in HTML. R package version 1.2. https://CRAN.R-project.org/package=table1 |
| survminer | 0.4.8 | Alboukadel Kassambara, Marcin Kosinski and Przemyslaw Biecek (2020). survminer: Drawing Survival Curves using ‘ggplot2’. R package version 0.4.8. https://CRAN.R-project.org/package=survminer |
| survival | 3.2-3 | Terry M. Therneau, Patricia M. Grambsch (2000). _Modeling Survival Data: Extending the Cox Model_. Springer, New York. ISBN 0-387-98784-3 |
| survivalROC | 1.0.3 | Patrick J. Heagerty and packaging by Paramita Saha-Chaudhuri (2013). survivalROC: Time-dependent ROC curve estimation from censored survival data. R package version 1.0.3. https://CRAN.R-project.org/package=survivalROC |
| WGCNA | 1.69 | Langfelder P and Horvath S, WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008, 9:559 doi:10.1186/1471-2105-9-559 |
| ggpubr | 0.4.0 | Alboukadel Kassambara (2020). ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.4.0. https://CRAN.R-project.org/package=ggpubr |
| limma | 3.44.3 | Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47. |
| randomForestSRC | 2.9.3 | Ishwaran H. and Kogalur U.B. (2007). Random survival forests for R. R News 7(2), 25–31. |
| mlr | 2.18.0 | Bischl B, Lang M, Kotthoff L, Schiffner J, Richter J, Studerus E, Casalicchio G, Jones Z (2016). “mlr: Machine Learning in R.” _Journal of Machine Learning Research_, *17*(170), 1-5. <URL: https://jmlr.org/papers/v17/15-066.html>. |
| enrichplot | 1.10.2 | Guangchuang Yu (2021). enrichplot: Visualization of Functional Enrichment Result. R package version 1.10.2. https://yulab-smu.top/biomedical-knowledge-mining-book/ |
| rms | 6.0-1 | Frank E Harrell Jr (2020). rms: Regression Modeling Strategies. R package version 6.0-1. https://CRAN.R-project.org/package=rms |
| TCGAbiolinks | 1.14.0 | Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Claudia Cava, Davide Garolini, Thais Sabedot, Tathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni,Michele Ceccarelli, Gianluca Bontempi Houtan Noushmehr. TCGAbiolinks: An R/Bioconductor package for integrative analysis of TCGA data Nucleic Acids Research (05 May 2016) 44 (8): e71. (doi:10.1093/nar/gkv1507) |
| ReactomePA | 1.34.0 | Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479 |
| clusterProfiler | 3.18.1 | Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology 2012, 16(5):284-287 |
| msigdbr | 7.1.1 | Igor Dolgalev (2020). msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format. R package version 7.1.1. https://CRAN.R-project.org/package=msigdbr |
| caret | 6.0-86 | Max Kuhn (2020). caret: Classification and Regression Training. R package version 6.0-86. https://CRAN.R-project.org/package=caret |