AltAnalyze Home Page
	AltAnalyze Tutorials
Section 1 - Introduction
	1.1 Program Description
	1.2 Updates
	1.3 Implementation
	1.4 Requirements
	1.5 Installation
	1.6 Pre-Processing, External Files and Applications
	1.7 Help with AltAnalyze
Section 2 - Running AltAnalyze
	2.1 Where to Save Input Expression Files?
	2.2 Beginning an AltAnalyze Run
	2.3 Running AltAnalyze from Command-Line
	2.4 AltAnalyze Analysis Options
	2.5 Overview of Analysis Results
	2.6 Additional à la carte Analyses
	2.7 AltAnalyze Results Viewer
Section 3 - Algorithms
	3.1 Default Methods
	3.2 Algorithm Descriptions
	3.3 Probe set Filtering
	3.4 Constitutive and gene expression calculation
	3.5 Alternative Splicing Prediction
	3.6 Protein/RNA Inference Analysis
	3.7 Gene Annotation Assignment
Section 4 - Using R with AltAnalyze
	4.1 Configuring R
Section 5 - Software Infrastructure
	5.1 Overview
	5.2 ExpressionBuilder Module
Section 6 - Building AltAnalyze Annotation Files
	6.1 Splicing Annotations and Protein Associations
	6.2 Building Ensembl-Exon Associations
	6.3 Extracting UniProt Protein Domain Annotations Overview
	6.4 Extracting Ensembl Protein Domain Annotations Overview
	6.5 Extracting microRNA Binding Annotations Overview
	6.6 Inferring Protein-Exon Associations Overview
	6.7 Required Files for Manual Update
Section 7 - Evaluation of AltAnalyze Predictions
Section 8 - Analysis of AltAnalyze Results DomainGraph