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1. Introduction
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VAMP
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VAMP
Contents
1. Introduction
2. Administration manual
2.1 System requirements
2.2 Installation and configuration
2.2.1 Installation
2.2.2 How to launch VAMP
2.2.3 Configuration
2.2.4 Data format
3. User Manual
3.1 Overview
3.1.1 Top-left frame
3.1.2 Bottom-left frame
3.1.3 Main frame
3.2 Basic functions
3.2.1 Data import
3.2.2 Data display
3.2.3 Search
3.2.4 Visual rendering
3.2.5 Print
3.2.6 Save and load
3.3 Data analysis
3.3.1 Manual analysis
3.3.2 FrAGL (Frequency of Amplicon, Gain and Loss) view
3.3.3 Finding common alterations among a collection of CGH- array profiles
3.3.4 Clustering profiles
3.3.5 Comparing profiles
3.3.6 Confrontation with sample annotation
3.3.7 Synteny analysis
3.3.8 Confrontation with Genome Annotation
3.3.9 Signal Histogram
3.3.10 Differential Analysis
3.3.11 Correlation Analysis
4. Analysis example - Bladder Cancer
4.1 Introduction
4.2 Import the genomic profiles
4.3 Minimal Alteration computation
4.3.1 Parameters settings
4.3.2 Visualization of the regions
4.3.3 Visualization of the samples with the alteration
4.3.4 Candidate genes
4.4 Genome/Transcriptome comparison
5. Analysis example - Colon Cancer
5.1 Introduction
5.2 Import the genomic profiles
5.3 Frequency alteration computation
5.3.1 Computation for each dataset
5.3.2 Comparison of the frequency between the two datasets
6. Availability
7. How to cite us?
Bibliography
8. Annexes
8.1 Main configuration XML file
8.2 Sample user configuration XML file
8.3 Import XML file
8.4 CGH array XML file
8.5 Transcriptome array XML file
2007 - Institut Curie Bioinformatics unit
