December 6, 2016
TCGA Data
TCGA Bioconductor Packages
- TCGAbiolinks
- RTCGAToolbox
- RTCGA
- TCGA2STAT
- TCGA-Assembler
- MultiAssayExperiment
What does TCGAbrowser have to offer
- Analyses based on gene expression subsetting
- Analyses based on mutation subsetting
- Convenience wrappers for limma/voom RNAseq analysis, GSVA and Reactome pathway analysis
- Differential mutation and copy number analysis
- Survival analysis
- Visualization by heatmap, oncoprint-like plots
- Shiny app for automated analysis
TCGAbrowser workflow
TCGAbrowser app in action
Outlook
Differential methylation analysis
Differential miRNA analysis
Update to GDC GRCh38 harmonized data
Acknowledgements
University Hospital Zurich
Reinhard Dummer
Mitch Levesque
University of Zurich
Mark Robinson
Michael Baudis
ETH Nexus
Daniel Stekhoven
Michael Prummer
Bioconductor
Martin Morgan