TCGAbiolinks swMATH ID: 32619 Software Authors: Antonio Colaprico, Tiago Chedraoui Silva, Catharina Olsen, Luciano Garofano, Davide Garolini, Claudia Cava, Thais Sabedot, Tathiane Malta, Stefano M. Pagnotta, Isabella Castiglioni, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr Description: TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data. The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines. Homepage: https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html Dependencies: R Related Software: glmnet; DESeq2; FSCseq; NB.MClust; iClusterPlus; zinbwave; Salmon; RSEM; NbClust; svaseq; DEseq; NMF; edgeR; Bioconductor; mclust; CorShrink; palasso; ipflasso; TANDEM; SuperLearner Cited in: 4 Publications all top 5 Cited by 13 Authors 1 Azizi, Lamiae 1 Ciocănea-Teodorescu, Iuliana 1 Ibrahim, Joseph George 1 Jonker, Marianne A. 1 Lim, David K. 1 Menezes, Renée X. 1 Miecznikowski, Jeffrey C. 1 Ormerod, John T. 1 Rashid, Naim U. 1 Rauschenberger, Armin 1 Tritchler, David L. 1 Yu, Weichang 1 Zhang, Fan Cited in 4 Serials 1 Computational Statistics and Data Analysis 1 Statistical Applications in Genetics and Molecular Biology 1 Advances in Data Analysis and Classification. ADAC 1 The Annals of Applied Statistics Cited in 2 Fields 4 Statistics (62-XX) 2 Biology and other natural sciences (92-XX) Citations by Year