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# 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<br> 1.2. https://CRAN.R-project.org/package=table1
survminer | 0.4.8 | Alboukadel Kassambara, Marcin Kosinski and Przemyslaw Biecek (2020). survminer: Drawing<br> Survival Curves using 'ggplot2'. R package version 0.4.8.<br> https://CRAN.R-project.org/package=survminer
survival | 3.2-3 | Terry M. Therneau, Patricia M. Grambsch (2000). \_Modeling Survival Data: Extending the Cox<br>Model\_. Springer, New York. ISBN 0-387-98784-3
survivalROC | 1.0.3 | Patrick J. Heagerty and packaging by Paramita Saha-Chaudhuri (2013). survivalROC:<br> Time-dependent ROC curve estimation from censored survival data. R package version 1.0.3.<br> https://CRAN.R-project.org/package=survivalROC
WGCNA | 1.69 | Langfelder P and Horvath S, WGCNA: an R package for weighted correlation network analysis.<br> 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<br> 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<br> powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic<br> 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<br>(2016). "mlr: Machine Learning in R." \_Journal of Machine Learning Research\_, \*17\*(170), 1-5.<br><URL: https://jmlr.org/papers/v17/15-066.html>.
enrichplot | 1.10.2 | Guangchuang Yu (2021). enrichplot: Visualization of Functional Enrichment Result. R package<br> 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.<br> https://CRAN.R-project.org/package=rms
TCGAbiolinks | 1.14.0 | Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Claudia Cava,<br> Davide Garolini, Thais Sabedot, Tathiane Malta, Stefano M. Pagnotta, Isabella<br> Castiglioni,Michele Ceccarelli, Gianluca Bontempi Houtan Noushmehr. TCGAbiolinks: An<br> R/Bioconductor package for integrative analysis of TCGA data Nucleic Acids Research (05 May<br> 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<br> 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<br> comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology<br> 2012, 16(5):284-287
msigdbr | 7.1.1 | Igor Dolgalev (2020). msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format.<br> 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.<br> https://CRAN.R-project.org/package=caret