TCGAbiolinksGUI was created to help users without knowledge of programming to search, download and analyze TCGA data. This package offers an graphical user interface to the R/biocondcutor packages TCGAbiolinks and ELMER packages. Also, some other useful packages from bioconductor, such as ComplexHeatmap package has been used for data visualization.
To install the package from biocondcutor repository, please, use the code below.
source("https://bioconductor.org/biocLite.R")
biocLite("TCGAbiolinksGUI")To install the package from a binary package, please, use the code below.
# dependencies
devtools::install_github("BioinformaticsFMRP/TCGAbiolinks")
source("https://bioconductor.org/biocLite.R")
biocLite(c("pathview","clusterProfiler","ELMER"))
install.packages(c("shiny","readr","googleVis","shinydashboard"))
devtools::install_github("thomasp85/shinyFiles")
devtools::install_github("ebailey78/shinyBS", ref="shinyBS3")
devtools::install_github("daattali/shinyjs")
install.packages("~/TCGAbiolinksGUI_0.99.0_R_x86_64-pc-linux-gnu.tar.gz", repos = NULL, type = "source")The following commands should be used in order to start the graphical user interface.
library(TCGAbiolinksGUI)
TCGAbiolinksGUI()Please cite both TCGAbiolinks package and TCGAbiolinksGUI:
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Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, Sabedot T, Malta TM, Pagnotta SM, Castiglioni I, Ceccarelli M, Bontempi G and Noushmehr H. "TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data." Nucleic acids research (2015): gkv1507.
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TCGAbiolinksGUI: A Graphical User Interface to analyze TCGA data. Manuscript in preparation.
Also, if you have used ELMER analysis please cite:
- Yao, L., Shen, H., Laird, P. W., Farnham, P. J., & Berman, B. P. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome Biol 16 (2015): 105.
- Yao, Lijing, Benjamin P. Berman, and Peggy J. Farnham. "Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes." Critical reviews in biochemistry and molecular biology 50.6 (2015): 550-573.
If you have used OncoPrint plot and Heatmap Plot please cite:
- Gu, Zuguang, Roland Eils, and Matthias Schlesner. "Complex heatmaps reveal patterns and correlations in multidimensional genomic data." Bioinformatics (2016): btw313
If you have used Pathway plot please cite:
- Luo, Weijun, Brouwer and Cory (2013). “Pathview: an R/Bioconductor package for pathway-based data integration and visualization.” Bioinformatics, 29(14), pp. 1830-1831.