Inhalt

•  
   Dedication
•  
   Abstract
•  
   Zusammenfassung
•  
   Publications
•  
   Acknowledgments
•  
   Contents
•  
   List of Figures
•  
   List of Tables
•  
   Acronyms
•  
    Data Mining and Visualization
•  
  1 Introduction
•  
   1.1 A brief history of data and visualization
•  
   1.2 Designing a visualization
•  
   1.2.1 What is to be visualized
•  
   1.2.2 Why visualize it
•  
   1.2.3 How to visualize it
•  
   2 Thesis overview
•  
   2.1 Motivation of the thesis
•  
   2.2 Structure of the thesis
•  
   3 A mnemonic card game for your amino acids
•  
   3.1 Background
•  
   3.2 Related work
•  
   3.3 Methodology
•  
   3.4 The problem
•  
   3.5 The solution
•  
   3.5.1 Process for developing the solution
•  
   3.5.2 Visual encoding
•  
   3.5.3 Key milestones
•  
   3.6 Results
•  
   3.7 Discussion
•  
    Presymptomatic Diagnosis of Oral Cancer
•  
  4 Biological background
•  
   4.1 Diversity and dynamics of cancer
•  
   4.1.1 Mutations
•  
   4.1.2 Copy number aberrations
•  
   4.1.3 Allelic imbalance
•  
   4.1.4 Cancer precursors
•  
   4.1.5 Oral cancer
•  
  4.2 Detecting allelic imbalances
•  
   4.2.1 Amplifying DNA
•  
   4.2.2 Digital PCR
•  
   4.2.3 Droplet digital PCR
•  
   4.3 Detecting CNAs with ddPCR
•  
   5 The ddPCRclust package
•  
   5.1 Related work
•  
   5.2 Problem statement
•  
  5.3 Methods
•  
   5.3.1 Input data
•  
   5.3.2 Step 1: Clustering
•  
   5.3.3 Step 2: Cluster labeling
•  
   5.3.4 Step 3: Rain allocation
•  
   5.3.5 Step 4: CPDs calculation
•  
  6 ddPCRclust Results
•  
   6.1 Results
•  
   6.2 Discussion
•  
   6.3 Outlook
•  
   7 The Visual Interface ddPCRvis
•  
  7.1 Implementation
•  
   7.1.1 Structure of a Shiny application
•  
   7.1.2 Reactive programming
•  
  7.2 The web interface
•  
   7.2.1 Upload files
•  
   7.2.2 Clustering
•  
   7.2.3 Edit clustering
•  
   7.2.4 Counts
•  
   7.2.5 CPDs
•  
   7.2.6 Result
•  
   7.2.7 Dynamic help system
•  
   7.3 Discussion
•  
   7.4 Outlook
•  
    Omics Fusion — A Platform for Integrative Analysis of Omics Data
•  
  8 Introducing Omics Fusion
•  
   8.1 Motivation
•  
   8.2 Omics techniques
•  
   8.2.1 Genomics
•  
   8.2.2 Transcriptomics
•  
   8.2.3 Proteomics
•  
   8.2.4 Metabolomics
•  
   8.3 Related work
•  
   8.4 Implementation
•  
  8.5 Functionality
•  
   8.5.1 Data manipulation
•  
   8.5.2 Data analysis
•  
   8.5.3 Visualization methods
•  
   8.5.4 Pathway map
•  
   9 Visualization of functional annotation data
•  
  9.1 Functional annotation
•  
   9.1.1 Gene Ontology
•  
   9.1.2 Clusters of Orthologous Groups
•  
   9.2 Semantic reasoner
•  
  9.3 The visualization
•  
   9.3.1 Box-and-whisker plots
•  
   9.3.2 COG/GO box plots
•  
   9.4 Discussion
•  
   9.5 Outlook
•  
   10 Conclusion
•  
   Quote
•  
    Individual Contributions
•  
    Bibliography
•  
   Colophon